Using VCF file directly

[emmannaemeka]

@matted @tw164 Can I use VCF file directly as input file?

[tw164]

Direct input from a VCF file is not currently implemented. For input to Multipool, pooled variant data in a VCF file must first be converted to an allele counts file in the tabular format described here.

Extracting allele counts/depths from pooled VCF data is not necessarily straightforward, because different variant-calling tools have used different tags to indicate allele depths, and it was only relatively recently, with version 4.3 of the VCF specification, that the 'AD' allele depth field was added as a reserved field.

I have written a prep script (mp_prep.py) that is included in a forked version of this package, which can be found here. This script can be called as follows:

python2 mp_prep.py -p POOL -f FOUNDER1,FOUNDER2 -r chr01 -o allele_counts.txt input.vcf

…where input.vcf is the name of an input VCF file, POOL is the name of a pool sample in the input VCF, FOUNDER1 and FOUNDER2 are the names of founder samples, chr01 is the name of a chromosome for which allele counts are to be generated, and allele_counts.txt is the resulting allele counts file that can be passed as input to the main Multipool script (mp_inference.py).

Note that this prep script expects two founders (as does Multipool), and makes use only of homozygous SNP genotypes that are segregating with respect to those two founders. The prep script also assumes that allele-depth tag sets are one of two types: the 'AO' and 'RO' tags used by FreeBayes, or the 'AD' tag used by GATK and by the VCF specification since version 4.3.

[emmannaemeka]

[SNP example.zip](https://github.com/matted/multipool/files/1613098/SNP.example.zip) Hello Dr Walsh, Thanks for the detailed description. Please am new to bioinformatics. I have attached an excerpt from the VCF generated using freeBayes. This is for one pool(F1 Population). So from this how do i fit it into this script python2 mp_prep.py -p POOL -f FOUNDER1,FOUNDER2 -r chr01 -o allele_counts.txt input.vcf Whats my founders? etc? Please bear with me. Thanks Nnadi Nnaemeka Emmanuel Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

…

On Mon, Jan 8, 2018 at 9:07 PM, TAB Walsh ***@***.***> wrote: Direct input from a VCF file is not currently implemented. For input to Multipool, pooled variant data in a VCF file must first be converted to an allele counts file in the tabular format described here <https://github.com/matted/multipool/wiki#user-content-forming-input-data> . Extracting allele counts/depths from pooled VCF data is not necessarily straightforward, because different variant-calling tools have used different tags to indicate allele depths, and it was only relatively recently, with version 4.3 of the VCF specification, that the 'AD' allele depth field was added as a reserved field. I have written a prep script (mp_prep.py) that is included in a forked version of this package, which can be found here <https://github.com/gact/multipool/>. This script can be called as follows: python2 mp_prep.py -p POOL -f FOUNDER1,FOUNDER2 -r chr01 -o allele_counts.txt input.vcf …where input.vcf is the name of an input VCF file, POOL is the name of a pool sample in the input VCF, FOUNDER1 and FOUNDER2 are the names of founder samples, chr01 is the name of a chromosome for which allele counts are to be generated, and allele_counts.txt is the resulting allele counts file that can be passed as input to the main Multipool script ( mp_inference.py). Note that this prep script expects two founders (as does Multipool), and makes use only of homozygous SNP genotypes that are segregating with respect to those two founders. The prep script also assumes that allele-depth tag sets are one of two types: the 'AO' and 'RO' tags used by FreeBayes, or the 'AD' tag used by GATK and by the VCF specification since version 4.3. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/matted/multipool/issues/10#issuecomment-356080812>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Aeq253GWPHXlLpW3LUAJ8EZlUN46FzDXks5tInVqgaJpZM4RWpA2> .

[emmannaemeka]

Error with python2 mp_prep.py

multipool-master emmannaemeka$ python2 mp_prep.py -p POOL -f FOUNDER1,FOUNDER2 -r chr01 -o allele_counts.txt input.vcf
Traceback (most recent call last):
File "mp_prep.py", line 30, in
import pysam
ImportError: No module named pysam

[tw164]

Hello Emmanuel,

The Python error occurs because the PySAM Python module couldn't be found. The PySAM module is used by mp_prep.py for accessing VCF input files. PySAM can be installed by following the instructions here.

For preparing Multipool input, you will need SNP genotype data for the pool sample (named POOL in the example command), as well as SNP genotypes for the founders (in the case of an F1 population, these are the parents). These are used by mp_prep.py to encode allele depth in terms of parental alleles.

If you would be so kind as to paste an excerpt from your VCF in plain text, I would be happy to have a look at it. Anything from the body of the VCF file — lines not begin with a number sign (#) — would be great.

Regards,

Thomas.

[emmannaemeka]

@tw164 Please find an excerpt of the vcd file from one of the pool
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
cneoH99_Chr1 99 . T C 38619.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1081;CIGAR=1X;DP=1081;DPB=1081;DPRA=0;EPP=4.26578;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1503.19;PAIRED=0.93247;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43044;QR=0;RO=0;RPL=490;RPP=23.5017;RPPR=0;RPR=591;RUN=1;SAF=569;SAP=9.53677;SAR=512;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1081:1081,1081:0:0:1081:43044:-3869.66,-325.413,0
cneoH99_Chr1 161 . C G 39966.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1125;CIGAR=1X;DP=1126;DPB=1126;DPRA=0;EPP=3.86152;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=59.9956;MQMR=0;NS=1;NUMALT=1;ODDS=1564.19;PAIRED=0.962667;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44520;QR=0;RO=0;RPL=583;RPP=6.25496;RPPR=0;RPR=542;RUN=1;SAF=585;SAP=6.91895;SAR=540;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1126:1126,1125:0:0:1125:44520:-4002.33,-338.659,0
cneoH99_Chr1 168 . T C 38630.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1083;CIGAR=1X;DP=1084;DPB=1084;DPRA=0;EPP=7.07053;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=59.9815;MQMR=0;NS=1;NUMALT=1;ODDS=1505.96;PAIRED=0.962142;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43051;QR=0;RO=0;RPL=578;RPP=13.6952;RPPR=0;RPR=505;RUN=1;SAF=567;SAP=8.22544;SAR=516;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1084:1084,1083:0:0:1083:43051:-3869.9,-326.015,0
cneoH99_Chr1 222 . G A 18119.4 . AB=0.5884;ABP=75.5708;AC=1;AF=0.5;AN=2;AO=629;CIGAR=1X;DP=1069;DPB=1069;DPRA=0;EPP=3.59373;EPPR=4.61659;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=59.968;NS=1;NUMALT=1;ODDS=2804.58;PAIRED=0.980922;PAIREDR=0.977169;PAO=0;PQA=0;PQR=0;PRO=0;QA=23902;QR=17295;RO=438;RPL=332;RPP=7.23932;RPPR=4.99338;RPR=297;RUN=1;SAF=317;SAP=3.09661;SAR=312;SRF=221;SRP=3.08962;SRR=217;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1069:1069,629:438:17295:629:23902:-1827.99,0,-1233.71
cneoH99_Chr1 262 . TGCAT CGCAA 36434.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=998;CIGAR=1X3M1X;DP=999;DPB=1029.6;DPRA=0;EPP=4.0634;EPPR=0;GTI=0;LEN=5;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1430.41;PAIRED=0.980962;PAIREDR=0;PAO=61;PQA=2147;PQR=0;PRO=0;QA=38434;QR=0;RO=0;RPL=508;RPP=3.71527;RPPR=0;RPR=490;RUN=1;SAF=496;SAP=3.08863;SAR=502;SRF=0;SRP=0;SRR=0;TYPE=complex GT:DP:DPR:RO:QR:AO:QA:GL 1/1:999:999,998:0:0:998:38434:-3648.41,-318.791,0
cneoH99_Chr1 308 . G A 37370.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1068;CIGAR=1X;DP=1070;DPB=1070;DPRA=0;EPP=3.14043;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=59.9494;MQMR=60;NS=1;NUMALT=1;ODDS=1471.41;PAIRED=0.978464;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=41645;QR=34;RO=2;RPL=531;RPP=3.0835;RPPR=7.35324;RPR=537;RUN=1;SAF=547;SAP=4.38475;SAR=521;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1070:1070,1068:2:34:1068:41645:-3740.27,-318.872,0
cneoH99_Chr1 365 . T A 38767.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1085;CIGAR=1X;DP=1085;DPB=1085;DPRA=0;EPP=3.58869;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.9908;MQMR=0;NS=1;NUMALT=1;ODDS=1508.73;PAIRED=0.980645;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=43183;QR=0;RO=0;RPL=552;RPP=3.73279;RPPR=0;RPR=533;RUN=1;SAF=566;SAP=7.4313;SAR=519;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1085:1085,1085:0:0:1085:43183:-3882.14,-326.618,0
cneoH99_Chr1 388 . C T 14058.8 . AB=0.439531;ABP=38.2007;AC=1;AF=0.5;AN=2;AO=487;CIGAR=1X;DP=1108;DPB=1108;DPRA=0;EPP=3.22878;EPPR=3.06634;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3237.15;PAIRED=0.98768;PAIREDR=0.979032;PAO=0;PQA=0;PQR=0;PRO=0;QA=19484;QR=24802;RO=620;RPL=222;RPP=11.2548;RPPR=9.7909;RPR=265;RUN=1;SAF=247;SAP=3.22878;SAR=240;SRF=324;SRP=5.75616;SRR=296;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1108:1108,487:620:24802:487:19484:-1418.16,0,-1896.23
cneoH99_Chr1 416 . G A,T 36440.4 . AB=0.445837,0.554163;ABP=31.4727,31.4727;AC=1,1;AF=0.5,0.5;AN=2;AO=498,619;CIGAR=1X,1X;DP=1117;DPB=1117;DPRA=0,0;EPP=3.86494,5.20282;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=59.992,59.9677;MQMR=0;NS=1;NUMALT=2;ODDS=3337.04;PAIRED=0.987952,0.975767;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=19988,24471;QR=0;RO=0;RPL=233,316;RPP=7.47534,3.60316;RPPR=0;RPR=265,303;RUN=1,1;SAF=261,321;SAP=5.52188,4.86605;SAR=237,298;SRF=0;SRP=0;SRR=0;TYPE=snp,snp GT:DP:DPR:RO:QR:AO:QA:GL 1/2:1117:1117,498,619:0:0:498,619:19988,24471:-3660.58,-2013.79,-1863.87,-1647.19,0,-1460.85
cneoH99_Chr1 456 . G C 40779.5 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1147;CIGAR=1X;DP=1149;DPB=1149;DPRA=0;EPP=7.19232;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1581.58;PAIRED=0.986922;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=45433;QR=24;RO=2;RPL=582;RPP=3.55743;RPPR=3.0103;RPR=565;RUN=1;SAF=584;SAP=3.84519;SAR=563;SRF=1;SRP=3.0103;SRR=1;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1149:1149,1147:2:24:1147:45433:-4082.18,-343.603,0
cneoH99_Chr1 1027 . C T 19031.6 . AB=0.588571;ABP=74.5572;AC=1;AF=0.5;AN=2;AO=618;CIGAR=1X;DP=1050;DPB=1050;DPRA=0;EPP=3.69899;EPPR=8.15749;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9676;NS=1;NUMALT=1;ODDS=2807.59;PAIRED=0.990291;PAIREDR=0.986111;PAO=0;PQA=0;PQR=0;PRO=0;QA=24857;QR=17254;RO=432;RPL=299;RPP=4.41578;RPPR=4.6389;RPR=319;RUN=1;SAF=315;SAP=3.51627;SAR=303;SRF=227;SRP=5.44315;SRR=205;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1050:1050,618:432:17254:618:24857:-1918.69,0,-1235.28
cneoH99_Chr1 1182 . GAC AAT 19342.3 . AB=0.596459;ABP=89.7255;AC=1;AF=0.5;AN=2;AO=640;CIGAR=1X1M1X;DP=1073;DPB=1081.33;DPRA=0;EPP=3.22745;EPPR=3.85783;GTI=0;LEN=3;MEANALT=1;MQM=59.4688;MQMR=59.9515;NS=1;NUMALT=1;ODDS=2772.33;PAIRED=0.982812;PAIREDR=0.986143;PAO=10;PQA=329;PQR=98;PRO=6;QA=25164;QR=17126;RO=433;RPL=323;RPP=3.13245;RPPR=3.13567;RPR=317;RUN=1;SAF=319;SAP=3.02387;SAR=321;SRF=205;SRP=5.66321;SRR=228;TYPE=complex GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1073:1073,640:433:17126:640:25164:-1951.1,0,-1220.95
cneoH99_Chr1 1443 . C T 20475.9 . AB=0.604464;ABP=109.172;AC=1;AF=0.5;AN=2;AO=677;CIGAR=1X;DP=1120;DPB=1120;DPRA=0;EPP=3.27011;EPPR=3.32472;GTI=0;LEN=1;MEANALT=2;MQM=59.6499;MQMR=59.9208;NS=1;NUMALT=1;ODDS=2850.15;PAIRED=0.977843;PAIREDR=0.984163;PAO=0;PQA=0;PQR=0;PRO=0;QA=26804;QR=17740;RO=442;RPL=297;RPP=25.1067;RPPR=3.18716;RPR=380;RUN=1;SAF=344;SAP=3.39841;SAR=333;SRF=219;SRP=3.08891;SRR=223;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1120:1120,677:442:17740:677:26804:-2068.82,0,-1256.53
cneoH99_Chr1 1797 . G T 22115 . AB=0.59851;ABP=104.832;AC=1;AF=0.5;AN=2;AO=723;CIGAR=1X;DP=1208;DPB=1208;DPRA=0;EPP=3.03733;EPPR=7.60449;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3128.04;PAIRED=0.970954;PAIREDR=0.987603;PAO=0;PQA=0;PQR=0;PRO=0;QA=28870;QR=19366;RO=484;RPL=329;RPP=15.6997;RPPR=3.29744;RPR=394;RUN=1;SAF=385;SAP=9.64485;SAR=338;SRF=256;SRP=6.52773;SRR=228;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1208:1208,723:484:19366:723:28870:-2231.99,0,-1377.62
cneoH99_Chr1 1899 . A T 4195.65 . AB=0.213978;ABP=826.575;AC=1;AF=0.5;AN=2;AO=248;CIGAR=1X;DP=1159;DPB=1159;DPRA=0;EPP=3.88589;EPPR=8.73336;GTI=0;LEN=1;MEANALT=1;MQM=58.2339;MQMR=58.1471;NS=1;NUMALT=1;ODDS=966.083;PAIRED=0.979839;PAIREDR=0.980241;PAO=0;PQA=0;PQR=0;PRO=0;QA=9793;QR=36124;RO=911;RPL=121;RPP=3.32551;RPPR=17.1427;RPR=127;RUN=1;SAF=124;SAP=3.0103;SAR=124;SRF=465;SRP=3.87078;SRR=446;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:1159:1159,248:911:36124:248:9793:-514.681,0,-2847.69
cneoH99_Chr1 2033 . C T 3953.41 . AB=0.58042;ABP=19.0762;AC=1;AF=0.5;AN=2;AO=166;CIGAR=1X;DP=286;DPB=286;DPRA=0;EPP=38.3818;EPPR=11.7686;GTI=0;LEN=1;MEANALT=1;MQM=39.3735;MQMR=37.3833;NS=1;NUMALT=1;ODDS=578.344;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6574;QR=4806;RO=120;RPL=121;RPP=78.5671;RPPR=55.7771;RPR=45;RUN=1;SAF=12;SAP=266.779;SAR=154;SRF=16;SRP=143.143;SRR=104;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:286:286,166:120:4806:166:6574:-446.248,0,-281.31
cneoH99_Chr1 6368 . T A 5.93664e-13 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1X;DP=118;DPB=118;DPRA=0;EPP=3.0103;EPPR=5.03202;GTI=0;LEN=1;MEANALT=2;MQM=15;MQMR=30.4713;NS=1;NUMALT=1;ODDS=29.6209;PAIRED=0.633333;PAIREDR=0.988506;PAO=0;PQA=0;PQR=0;PRO=0;QA=1178;QR=3517;RO=87;RPL=18;RPP=5.61607;RPPR=14.0174;RPR=12;RUN=1;SAF=13;SAP=4.16842;SAR=17;SRF=43;SRP=3.03526;SRR=44;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/0:118:118,30:87:3517:30:1178:0,-0.608226,-135.641
cneoH99_Chr1 10411 . A G 77.3512 . AB=0.358974;ABP=9.74743;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=33.4109;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=29.6429;MQMR=59.12;NS=1;NUMALT=1;ODDS=17.8108;PAIRED=0.928571;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=552;QR=1008;RO=25;RPL=0;RPP=33.4109;RPPR=3.79203;RPR=14;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=9;SRP=7.26639;SRR=16;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:39:39,14:25:1008:14:552:-23.94,0,-79.1647
cneoH99_Chr1 10423 . C T 214.246 . AB=0.414634;ABP=5.60547;AC=1;AF=0.5;AN=2;AO=17;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=18.4661;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=33.7059;MQMR=59.0833;NS=1;NUMALT=1;ODDS=49.332;PAIRED=0.941176;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=688;QR=980;RO=24;RPL=0;RPP=39.9253;RPPR=3.37221;RPR=17;RUN=1;SAF=14;SAP=18.4661;SAR=3;SRF=9;SRP=6.26751;SRR=15;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:41:41,17:24:980:17:688:-34.2737,0,-76.0455
cneoH99_Chr1 10434 . C G 382.039 . AB=0.48;ABP=3.18402;AC=1;AF=0.5;AN=2;AO=24;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=8.80089;EPPR=6.01695;GTI=0;LEN=1;MEANALT=1;MQM=35.5833;MQMR=59.1538;NS=1;NUMALT=1;ODDS=87.9677;PAIRED=0.875;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=971;QR=1058;RO=26;RPL=0;RPP=55.1256;RPPR=6.01695;RPR=24;RUN=1;SAF=16;SAP=8.80089;SAR=8;SRF=10;SRP=6.01695;SRR=16;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:50:50,24:26:1058:24:971:-51.1117,0,-80.348
cneoH99_Chr1 10471 . C T 570.813 . AB=0.517241;ABP=3.16006;AC=1;AF=0.5;AN=2;AO=30;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=17.1973;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=34.9333;MQMR=51;NS=1;NUMALT=1;ODDS=131.435;PAIRED=0.9;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1209;QR=1126;RO=28;RPL=8;RPP=17.1973;RPPR=3.0103;RPR=22;RUN=1;SAF=16;SAP=3.29983;SAR=14;SRF=12;SRP=4.25114;SRR=16;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:58:58,30:28:1126:30:1209:-65.473,0,-73.6021
cneoH99_Chr1 10482 . T C 566.878 . AB=0.563636;ABP=4.94488;AC=1;AF=0.5;AN=2;AO=31;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=40.0654;EPPR=3.37221;GTI=0;LEN=1;MEANALT=1;MQM=33.9032;MQMR=49.5;NS=1;NUMALT=1;ODDS=120.199;PAIRED=0.903226;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1257;QR=942;RO=24;RPL=12;RPP=6.44263;RPPR=3.37221;RPR=19;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=10;SRP=4.45795;SRR=14;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:55:55,31:24:942:31:1257:-66.719,0,-57.9497
cneoH99_Chr1 10536 . C T 527.354 . AB=0.682927;ABP=14.9269;AC=1;AF=0.5;AN=2;AO=28;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.0103;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=34.7857;MQMR=42.3077;NS=1;NUMALT=1;ODDS=37.0965;PAIRED=0.892857;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1139;QR=533;RO=13;RPL=26;RPP=47.6806;RPPR=31.2394;RPR=2;RUN=1;SAF=12;SAP=4.25114;SAR=16;SRF=6;SRP=3.17734;SRR=7;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:41:41,28:13:533:28:1139:-64.4541,0,-25.4782
cneoH99_Chr1 10545 . C T 453.155 . AB=0.631579;ABP=8.7247;AC=1;AF=0.5;AN=2;AO=24;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=4.45795;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=42.1429;NS=1;NUMALT=1;ODDS=48.9657;PAIRED=0.875;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=976;QR=565;RO=14;RPL=22;RPP=39.2015;RPPR=25.3454;RPR=2;RUN=1;SAF=8;SAP=8.80089;SAR=16;SRF=6;SRP=3.63072;SRR=8;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:38:38,24:14:565:24:976:-55.8434,0,-29.2033
cneoH99_Chr1 12362 . TCCTCAT ATGTCAC 3.47052e-06 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=3X3M1X;DP=13;DPB=13.8571;DPRA=0;EPP=9.52472;EPPR=22.5536;GTI=0;LEN=7;MEANALT=2;MQM=14.6667;MQMR=29.3333;NS=1;NUMALT=1;ODDS=14.0398;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=36;PRO=1;QA=94;QR=365;RO=9;RPL=0;RPP=9.52472;RPPR=3.25157;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=complex GT:DP:DPR:RO:QR:AO:QA:GL 0/0:13:13,3:9:365:3:94:0,-0.118182,-21.5253
cneoH99_Chr1 12386 . CGA TGT 1.06417 . AB=0.411765;ABP=4.1599;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X1M1X;DP=17;DPB=17;DPRA=0;EPP=10.7656;EPPR=5.80219;GTI=0;LEN=3;MEANALT=2;MQM=17.4286;MQMR=30;NS=1;NUMALT=1;ODDS=1.28134;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=277;QR=287;RO=7;RPL=1;RPP=10.7656;RPPR=5.80219;RPR=6;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=4;SRP=3.32051;SRR=3;TYPE=complex GT:DP:DPR:RO:QR:AO:QA:GL 0/1:17:17,7:7:287:7:277:-6.75383,0,-14.0539
cneoH99_Chr1 12441 . A G 164.083 . AB=0.7;ABP=13.4334;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=15.5221;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=22.5238;MQMR=28.7778;NS=1;NUMALT=1;ODDS=15.535;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=804;QR=369;RO=9;RPL=5;RPP=15.5221;RPPR=3.25157;RPR=16;RUN=1;SAF=21;SAP=48.6112;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 0/1:30:30,21:9:369:21:804:-30.6314,0,-13.5949
cneoH99_Chr1 12448 . GAGGT CAGGC 253.019 . AB=0.647059;ABP=9.39698;AC=1;AF=0.5;AN=2;AO=22;CIGAR=1X3M1X;DP=34;DPB=35.4;DPRA=0;EPP=17.2236;EPPR=3.20771;GTI=0;LEN=5;MEANALT=2;MQM=24.4545;MQMR=32.2727;NS=1;NUMALT=1;ODDS=31.1268;PAIRED=1;PAIREDR=1;PAO=2;PQA=73;PQR=33;PRO=1;QA=885;QR=429;RO=11;RPL=4;RPP=22.3561;RPPR=4.78696;RPR=18;RUN=1;SAF=21;SAP=42.4916;SAR=1;SRF=10;SRP=19.0002;SRR=1;TYPE=complex GT:DP:DPR:RO:QR:AO:QA:GL 0/1:34:34,22:11:429:22:885:-39.1899,0,-20.8749

[emmannaemeka]

@tw164 CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
cneoH99_Chr1	99	.	T	C	50426.3	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1415;CIGAR=1X;DP=1415;DPB=1415;DPRA=0;EPP=6.6949;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.983;MQMR=0;NS=1;NUMALT=1;ODDS=1966.21;PAIRED=0.928622;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56243;QR=0;RO=0;RPL=619;RPP=51.0881;RPPR=0;RPR=796;RUN=1;SAF=781;SAP=36.1717;SAR=634;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1081:1081,1081:0:0:1081:43044:-3869.66,-325.413,0
cneoH99_Chr1	161	.	C	G	52460.3	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1487;CIGAR=1X;DP=1487;DPB=1487;DPRA=0;EPP=21.0027;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=2066.02;PAIRED=0.958978;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58459;QR=0;RO=0;RPL=795;RPP=18.5027;RPPR=0;RPR=692;RUN=1;SAF=787;SAP=14.0633;SAR=700;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1126:1126,1125:0:0:1125:44520:-4002.33,-338.659,0
cneoH99_Chr1	168	.	T	C	53275.2	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1494;CIGAR=1X;DP=1496;DPB=1496;DPRA=0;EPP=38.3818;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2059.11;PAIRED=0.959839;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=59417;QR=44;RO=2;RPL=811;RPP=26.8238;RPPR=7.35324;RPR=683;RUN=1;SAF=780;SAP=9.34158;SAR=714;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1084:1084,1083:0:0:1083:43051:-3869.9,-326.015,0
cneoH99_Chr1	222	.	G	A	24631.6	.	AB=0.595788;ABP=120.323;AC=1;AF=0.5;AN=2;AO=877;CIGAR=1X;DP=1472;DPB=1472;DPRA=0;EPP=5.38976;EPPR=3.83144;GTI=0;LEN=1;MEANALT=1;MQM=59.9852;MQMR=59.9866;NS=1;NUMALT=1;ODDS=3791.54;PAIRED=0.973774;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=32548;QR=23470;RO=595;RPL=438;RPP=3.01278;RPPR=3.18913;RPR=439;RUN=1;SAF=435;SAP=3.13163;SAR=442;SRF=281;SRP=6.98464;SRR=314;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1069:1069,629:438:17295:629:23902:-1827.99,0,-1233.71
cneoH99_Chr1	262	.	TGCAT	CGCAA	48506.1	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1334;CIGAR=1X3M1X;DP=1335;DPB=1373;DPRA=0;EPP=3.5377;EPPR=0;GTI=0;LEN=5;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1908.68;PAIRED=0.976012;PAIREDR=0;PAO=79;PQA=2757;PQR=0;PRO=0;QA=51256;QR=0;RO=0;RPL=667;RPP=3.0103;RPPR=0;RPR=667;RUN=1;SAF=637;SAP=8.87035;SAR=697;SRF=0;SRP=0;SRR=0;TYPE=complex	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:999:999,998:0:0:998:38434:-3648.41,-318.791,0
cneoH99_Chr1	308	.	G	A	50557.7	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1445;CIGAR=1X;DP=1447;DPB=1447;DPRA=0;EPP=4.1058;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=59.9896;MQMR=60;NS=1;NUMALT=1;ODDS=1998.22;PAIRED=0.978547;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=56314;QR=27;RO=1;RPL=740;RPP=4.85117;RPPR=5.18177;RPR=705;RUN=1;SAF=724;SAP=3.02382;SAR=721;SRF=1;SRP=5.18177;SRR=0;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1070:1070,1068:2:34:1068:41645:-3740.27,-318.872,0
cneoH99_Chr1	365	.	T	A	52245	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1456;CIGAR=1X;DP=1458;DPB=1458;DPRA=0;EPP=3.60686;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=59.9794;MQMR=0;NS=1;NUMALT=1;ODDS=2023.05;PAIRED=0.980769;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58182;QR=0;RO=0;RPL=715;RPP=4.01848;RPPR=0;RPR=741;RUN=1;SAF=759;SAP=8.74323;SAR=697;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1085:1085,1085:0:0:1085:43183:-3882.14,-326.618,0
cneoH99_Chr1	388	.	C	T	16783.2	.	AB=0.390992;ABP=161.131;AC=1;AF=0.5;AN=2;AO=599;CIGAR=1X;DP=1532;DPB=1532;DPRA=0;EPP=3.44894;EPPR=4.96765;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3864.49;PAIRED=0.986644;PAIREDR=0.982851;PAO=0;PQA=0;PQR=0;PRO=0;QA=24072;QR=37240;RO=933;RPL=280;RPP=8.52417;RPPR=15.4131;RPR=319;RUN=1;SAF=305;SAP=3.44894;SAR=294;SRF=499;SRP=12.8436;SRR=434;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1108:1108,487:620:24802:487:19484:-1418.16,0,-1896.23
cneoH99_Chr1	416	.	G	A,T	49899	.	AB=0.374432,0.624919;ABP=214.055,211.879;AC=1,1;AF=0.5,0.5;AN=2;AO=577,963;CIGAR=1X,1X;DP=1541;DPB=1541;DPRA=0,0;EPP=4.66995,3.06667;EPPR=5.18177;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,59.9792;MQMR=60;NS=1;NUMALT=2;ODDS=3625;PAIRED=0.989601,0.983385;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=22998,38075;QR=12;RO=1;RPL=292,496;RPP=3.19471,4.90667;RPPR=5.18177;RPR=285,467;RUN=1,1;SAF=297,526;SAP=4.09792,20.8714;SAR=280,437;SRF=0;SRP=5.18177;SRR=1;TYPE=snp,snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/2:1117:1117,498,619:0:0:498,619:19988,24471:-3660.58,-2013.79,-1863.87,-1647.19,0,-1460.85
cneoH99_Chr1	456	.	G	C	54969.4	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1542;CIGAR=1X;DP=1544;DPB=1544;DPRA=0;EPP=8.77836;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQM=59.9994;MQMR=0;NS=1;NUMALT=1;ODDS=2142.27;PAIRED=0.978599;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61222;QR=0;RO=0;RPL=785;RPP=4.11434;RPPR=0;RPR=757;RUN=1;SAF=808;SAP=10.7217;SAR=734;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	1/1:1149:1149,1147:2:24:1147:45433:-4082.18,-343.603,0
cneoH99_Chr1	1027	.	C	T	25058.3	.	AB=0.549704;ABP=35.6053;AC=1;AF=0.5;AN=2;AO=835;CIGAR=1X;DP=1519;DPB=1519;DPRA=0;EPP=11.4595;EPPR=6.26116;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4568.61;PAIRED=0.978443;PAIREDR=0.980994;PAO=0;PQA=0;PQR=0;PRO=0;QA=33097;QR=27293;RO=684;RPL=416;RPP=3.03371;RPPR=6.68022;RPR=419;RUN=1;SAF=416;SAP=3.03371;SAR=419;SRF=355;SRP=5.15638;SRR=329;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1050:1050,618:432:17254:618:24857:-1918.69,0,-1235.28
cneoH99_Chr1	1182	.	GAC	AAT	22800.7	.	AB=0.533333;ABP=16.6182;AC=1;AF=0.5;AN=2;AO=752;CIGAR=1X1M1X;DP=1410;DPB=1434;DPRA=0;EPP=9.66332;EPPR=4.47231;GTI=0;LEN=3;MEANALT=3;MQM=59.6782;MQMR=59.9878;NS=1;NUMALT=1;ODDS=4339.67;PAIRED=0.970745;PAIREDR=0.984733;PAO=30;PQA=1042;PQR=346;PRO=15;QA=29305;QR=25592;RO=655;RPL=371;RPP=3.29906;RPPR=6.19623;RPR=381;RUN=1;SAF=379;SAP=3.11425;SAR=373;SRF=334;SRP=3.57057;SRR=321;TYPE=complex	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1073:1073,640:433:17126:640:25164:-1951.1,0,-1220.95
cneoH99_Chr1	1443	.	C	T	25570.5	.	AB=0.572003;ABP=70.2416;AC=1;AF=0.5;AN=2;AO=854;CIGAR=1X;DP=1493;DPB=1493;DPRA=0;EPP=5.00378;EPPR=3.28556;GTI=0;LEN=1;MEANALT=1;MQM=59.6417;MQMR=60;NS=1;NUMALT=1;ODDS=4186.99;PAIRED=0.982436;PAIREDR=0.976526;PAO=0;PQA=0;PQR=0;PRO=0;QA=33746;QR=25391;RO=639;RPL=369;RPP=37.225;RPPR=3.0137;RPR=485;RUN=1;SAF=436;SAP=3.83414;SAR=418;SRF=314;SRP=3.42149;SRR=325;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1120:1120,677:442:17740:677:26804:-2068.82,0,-1256.53
cneoH99_Chr1	1797	.	G	T	24735.6	.	AB=0.542857;ABP=27.0206;AC=1;AF=0.5;AN=2;AO=817;CIGAR=1X;DP=1505;DPB=1505;DPRA=0;EPP=4.94788;EPPR=3.08932;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4571.08;PAIRED=0.982864;PAIREDR=0.975255;PAO=0;PQA=0;PQR=0;PRO=0;QA=32692;QR=27252;RO=687;RPL=383;RPP=9.9234;RPPR=14.7717;RPR=434;RUN=1;SAF=436;SAP=11.0503;SAR=381;SRF=352;SRP=3.92377;SRR=335;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1208:1208,723:484:19366:723:28870:-2231.99,0,-1377.62
cneoH99_Chr1	1899	.	A	T	4195.65	.	AB=0.213978;ABP=826.575;AC=1;AF=0.5;AN=2;AO=248;CIGAR=1X;DP=1159;DPB=1159;DPRA=0;EPP=3.88589;EPPR=8.73336;GTI=0;LEN=1;MEANALT=1;MQM=58.2339;MQMR=58.1471;NS=1;NUMALT=1;ODDS=966.083;PAIRED=0.979839;PAIREDR=0.980241;PAO=0;PQA=0;PQR=0;PRO=0;QA=9793;QR=36124;RO=911;RPL=121;RPP=3.32551;RPPR=17.1427;RPR=127;RUN=1;SAF=124;SAP=3.0103;SAR=124;SRF=465;SRP=3.87078;SRR=446;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:1159:1159,248:911:36124:248:9793:-514.681,0,-2847.69
cneoH99_Chr1	2033	.	C	T	4293.25	.	AB=0.538244;ABP=7.49473;AC=1;AF=0.5;AN=2;AO=190;CIGAR=1X;DP=353;DPB=353;DPRA=0;EPP=19.5135;EPPR=11.3365;GTI=0;LEN=1;MEANALT=1;MQM=37.9474;MQMR=38.7914;NS=1;NUMALT=1;ODDS=847.931;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7544;QR=6463;RO=163;RPL=126;RPP=46.9426;RPPR=52.5812;RPR=64;RUN=1;SAF=12;SAP=317.942;SAR=178;SRF=18;SRP=217.879;SRR=145;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:286:286,166:120:4806:166:6574:-446.248,0,-281.31
cneoH99_Chr1	6368	.	T	A	5.93664e-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1X;DP=118;DPB=118;DPRA=0;EPP=3.0103;EPPR=5.03202;GTI=0;LEN=1;MEANALT=2;MQM=15;MQMR=30.4713;NS=1;NUMALT=1;ODDS=29.6209;PAIRED=0.633333;PAIREDR=0.988506;PAO=0;PQA=0;PQR=0;PRO=0;QA=1178;QR=3517;RO=87;RPL=18;RPP=5.61607;RPPR=14.0174;RPR=12;RUN=1;SAF=13;SAP=4.16842;SAR=17;SRF=43;SRP=3.03526;SRR=44;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/0:118:118,30:87:3517:30:1178:0,-0.608226,-135.641
cneoH99_Chr1	10411	.	A	G	77.3512	.	AB=0.358974;ABP=9.74743;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=33.4109;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=29.6429;MQMR=59.12;NS=1;NUMALT=1;ODDS=17.8108;PAIRED=0.928571;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=552;QR=1008;RO=25;RPL=0;RPP=33.4109;RPPR=3.79203;RPR=14;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=9;SRP=7.26639;SRR=16;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:39:39,14:25:1008:14:552:-23.94,0,-79.1647
cneoH99_Chr1	10423	.	C	T	214.246	.	AB=0.414634;ABP=5.60547;AC=1;AF=0.5;AN=2;AO=17;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=18.4661;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=33.7059;MQMR=59.0833;NS=1;NUMALT=1;ODDS=49.332;PAIRED=0.941176;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=688;QR=980;RO=24;RPL=0;RPP=39.9253;RPPR=3.37221;RPR=17;RUN=1;SAF=14;SAP=18.4661;SAR=3;SRF=9;SRP=6.26751;SRR=15;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:41:41,17:24:980:17:688:-34.2737,0,-76.0455
cneoH99_Chr1	10434	.	C	G	382.039	.	AB=0.48;ABP=3.18402;AC=1;AF=0.5;AN=2;AO=24;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=8.80089;EPPR=6.01695;GTI=0;LEN=1;MEANALT=1;MQM=35.5833;MQMR=59.1538;NS=1;NUMALT=1;ODDS=87.9677;PAIRED=0.875;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=971;QR=1058;RO=26;RPL=0;RPP=55.1256;RPPR=6.01695;RPR=24;RUN=1;SAF=16;SAP=8.80089;SAR=8;SRF=10;SRP=6.01695;SRR=16;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:50:50,24:26:1058:24:971:-51.1117,0,-80.348
cneoH99_Chr1	10471	.	C	T	218.71	.	AB=0.203593;ABP=130.451;AC=1;AF=0.5;AN=2;AO=34;CIGAR=1X;DP=167;DPB=167;DPRA=0;EPP=7.09778;EPPR=4.98585;GTI=0;LEN=1;MEANALT=1;MQM=33.2353;MQMR=55.3158;NS=1;NUMALT=1;ODDS=50.3597;PAIRED=1;PAIREDR=0.977444;PAO=0;PQA=0;PQR=0;PRO=0;QA=1382;QR=5251;RO=133;RPL=11;RPP=12.2071;RPPR=14.9126;RPR=23;RUN=1;SAF=20;SAP=5.30951;SAR=14;SRF=69;SRP=3.41847;SRR=64;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:58:58,30:28:1126:30:1209:-65.473,0,-73.6021
cneoH99_Chr1	10482	.	T	C	277.38	.	AB=0.221519;ABP=109.44;AC=1;AF=0.5;AN=2;AO=35;CIGAR=1X;DP=158;DPB=158;DPRA=0;EPP=20.9405;EPPR=6.98251;GTI=0;LEN=1;MEANALT=1;MQM=32.7143;MQMR=54.6585;NS=1;NUMALT=1;ODDS=63.8691;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=1431;QR=4853;RO=123;RPL=15;RPP=4.56135;RPPR=15.8802;RPR=20;RUN=1;SAF=20;SAP=4.56135;SAR=15;SRF=65;SRP=3.87536;SRR=58;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:55:55,31:24:942:31:1257:-66.719,0,-57.9497
cneoH99_Chr1	10536	.	C	T	439.911	.	AB=0.309091;ABP=37.8328;AC=1;AF=0.5;AN=2;AO=34;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=7.09778;EPPR=22.325;GTI=0;LEN=1;MEANALT=1;MQM=32.6471;MQMR=51.3816;NS=1;NUMALT=1;ODDS=101.293;PAIRED=1;PAIREDR=0.986842;PAO=0;PQA=0;PQR=0;PRO=0;QA=1390;QR=3050;RO=76;RPL=30;RPP=46.1843;RPPR=36.0395;RPR=4;RUN=1;SAF=17;SAP=3.0103;SAR=17;SRF=30;SRP=10.3247;SRR=46;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:41:41,28:13:533:28:1139:-64.4541,0,-25.4782
cneoH99_Chr1	10545	.	C	T	360.202	.	AB=0.28;ABP=45.05;AC=1;AF=0.5;AN=2;AO=28;CIGAR=1X;DP=100;DPB=100;DPRA=0;EPP=5.80219;EPPR=17.6074;GTI=0;LEN=1;MEANALT=1;MQM=34.3214;MQMR=50.0694;NS=1;NUMALT=1;ODDS=82.9395;PAIRED=1;PAIREDR=0.986111;PAO=0;PQA=0;PQR=0;PRO=0;QA=1139;QR=2882;RO=72;RPL=22;RPP=22.8638;RPPR=26.6552;RPR=6;RUN=1;SAF=11;SAP=5.80219;SAR=17;SRF=25;SRP=17.6074;SRR=47;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:38:38,24:14:565:24:976:-55.8434,0,-29.2033
cneoH99_Chr1	12362	.	T	A	0.00134313	.	AB=0.275862;ABP=15.6647;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=3.0103;EPPR=20.4855;GTI=0;LEN=1;MEANALT=1;MQM=18.25;MQMR=31;NS=1;NUMALT=1;ODDS=8.08115;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=319;QR=774;RO=21;RPL=4;RPP=3.0103;RPPR=3.94093;RPR=4;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:29:29,8:21:774:8:319:-4.12212,0,-46.0364
cneoH99_Chr1	12362	.	TCCTCAT	ATGTCAC	3.47052e-06	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=3X3M1X;DP=13;DPB=13.8571;DPRA=0;EPP=9.52472;EPPR=22.5536;GTI=0;LEN=7;MEANALT=2;MQM=14.6667;MQMR=29.3333;NS=1;NUMALT=1;ODDS=14.0398;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=36;PRO=1;QA=94;QR=365;RO=9;RPL=0;RPP=9.52472;RPPR=3.25157;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=complex	GT:DP:DPR:RO:QR:AO:QA:GL	0/0:13:13,3:9:365:3:94:0,-0.118182,-21.5253
cneoH99_Chr1	12386	.	CGA	TGT	3.21407e-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X1M1X;DP=36;DPB=36.3333;DPRA=0;EPP=4.09604;EPPR=12.7417;GTI=0;LEN=3;MEANALT=2;MQM=10.875;MQMR=32.5185;NS=1;NUMALT=1;ODDS=27.9352;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=32;PRO=1;QA=308;QR=1047;RO=27;RPL=5;RPP=4.09604;RPPR=6.95112;RPR=3;RUN=1;SAF=8;SAP=20.3821;SAR=0;SRF=17;SRP=6.95112;SRR=10;TYPE=complex	GT:DP:DPR:RO:QR:AO:QA:GL	0/1:17:17,7:7:287:7:277:-6.75383,0,-14.0539
cneoH99_Chr1	12441	.	A	G

[tw164]

Is this your pooled sample? It looks fine for preparing Multipool input, as it has the RO/AO tag set used by FreeBayes to indicate the number of reference and alternate allele observations.

However, there is one missing piece: genotype data for the founders/parents — required for assigning alleles to a specific parent. Given data for two parents of the F1 cross (say, PARENT1 and PARENT2) that are stored in a VCF file (say, parents.vcf), the command to prepare these for Multipool might be as follows:

python2 mp_prep.py -p unknown -f PARENT1,PARENT2 -r cneoH99_Chr1 -o allele_counts.txt input.vcf parents.vcf

…where unknown is the name of the pooled sample contained in input.vcf, PARENT1 and PARENT2 are the names of the parent samples contained in parents.vcf, cneoH99_Chr1 is the chromosome of interest, and allele_counts.txt is the output allele counts file.

[emmannaemeka]

Please a clarification 1.Parents.vcf should it be a combination of parent1 and Parent2 2. input.vcf should it be combination of high and low pool? 3. unknown is it same as input.vcf Thanks for your patience Nnadi Nnaemeka Emmanuel Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/ publications

…

On Jan 9, 2018 7:51 AM, "TAB Walsh" ***@***.***> wrote: Is this your pooled sample? It looks fine for preparing Multipool input, as it has the RO/AO tag set used by FreeBayes to indicate the number of reference and alternate allele observations. However, there is one missing piece: genotype data for the founders/parents — required for assigning alleles to a specific parent. Given data for two parents of the F1 cross (say, PARENT1 and PARENT2) that are stored in a VCF file (say, parents.vcf), the command to prepare these for Multipool might be as follows: python2 mp_prep.py -p unknown -f PARENT1,PARENT2 -r cneoH99_Chr1 -o allele_counts.txt input.vcf parents.vcf …where unknown is the name of the pooled sample contained in input.vcf, PARENT1 and PARENT2 are the names of the parent samples contained in parents.vcf, cneoH99_Chr1 is the chromosome of interest, and allele_counts.txt is the output allele counts file. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/matted/multipool/issues/10#issuecomment-356195941>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Aeq253tl0GUdBhqhNIzF_dk7S543M2F2ks5tIwx7gaJpZM4RWpA2> .

[emmannaemeka]

I ran this command line
python2 mp_prep.py -p /Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.txt -f /Users/emmannaemeka/Desktop/QTLcryptococcus/Parent1.txt,/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent2.txt -r cneoH99_Chr1 -o allele_counts.txt /Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.txt /Users/emmannaemeka/Desktop/QTLcryptococcus/Parents.vcf

This was the result

Python version: 2.7.13
Multipool version: 0.10.2
PySAM version: 0.13
Input variant file(s): /Users/emmannaemeka/Desktop/QTLcryptococcus/Parents.vcf:/Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.txt
Pool sample: /Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.txt
Founder sample(s): /Users/emmannaemeka/Desktop/QTLcryptococcus/Parent1.txt,/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent2.txt
Region(s): cneoH99_Chr1
Output allele depth file: allele_counts.txt
Checking for pool and founder samples in input variant data...
Sample '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent1.txt' found in input file(s):
Sample '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent2.txt' found in input file(s):
Sample '/Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.txt' found in input file(s):
Getting founder allele info...
Found 0 variants in region 'cneoH99_Chr1' of founders '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent1.txt' and '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent2.txt'...
Of these, 0 are SNPs...
Of these, 0 have homozygous genotypes...
Of these, 0 are segregating with respect to founders '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent1.txt' and '/Users/emmannaemeka/Desktop/QTLcryptococcus/Parent2.txt'...
Traceback (most recent call last):
File "mp_prep.py", line 490, in
sample_file_info, quiet=quiet)
File "mp_prep.py", line 361, in get_founder_allele_info
"for region '{}'".format(region))
RuntimeError: founder alleles not found for region 'cneoH99_Chr1'

[tw164]

In response to your questions:

1. Actually, mp_prep.py will accept any number of VCF files, and will extract genotype data only for the specified pool sample and its two parent samples. So you could pass one VCF file containing the pool and parent samples, one VCF containing the pooled sample and one containing both parent samples, or even a separate VCF file for each sample. All of these would be valid input.
2. The VCF file input to mp_prep.py can contain data for both high and low samples, but you would need to set parameter -p (the pool sample name) of either the high pool or the low pool. Each call to mp_prep.py script produces a single allele count file containing data for a single pool, which can then be input to the main Multipool script (mp_inference.py). If you have both a high and low pool, you will need to run mp_prep.py once for each pool, then input both allele count files simultaneously to mp_inference.py.
3. The text string in the rightmost column of the top row of your VCF excerpt, above the sample genotype data, is the sample name. In this example it is unknown, but it could just as easily be High_Pool, for example.

In response to the error, parameters -p and -f should be the names of the pool sample and founder samples, respectively. Please have a look at the help output for this script, which can be viewed with the following command:

python2 mp_prep.py -h

Before running this prep script, you will need to check the VCF data to find the names of the pool samples and the founder samples. These must then be specified when you run the script, so that it knows which samples are which.

[emmannaemeka]

Hi Matt I think I have a situation at hand for example this is the VCF for one of the pools my low bulk but i can't find the name of the pool on it(sample name) this is the same problem for all of them. So when i run this command line python2 mp_prep.py -p lowbulk,highbulk -f KN99a,EN28 -r cneoH99_Chr11 -o allele_counts.txt /Users/emmannaemeka/Desktop/QTLcryptococcus/Pool_combine.vcf /Users/emmannaemeka/Desktop/QTLcryptococcus/Parents_combined.vcf It returns negative. the sample name(lowbulk,highbulk KN99a,EN28) can't be found in the VCF file. how can i solve this find an exampled of the vcd file for the lowbulk ##fileformat=VCFv4.1 ##fileDate=20180108 ##source=freeBayes v1.0.2-29-g41c1313 ##reference=localref.fa ##contig=<ID=cneoH99_Chr1,length=2291499> ##contig=<ID=cneoH99_Chr2,length=1621675> ##contig=<ID=cneoH99_Chr3,length=1575141> ##contig=<ID=cneoH99_Chr4,length=1084805> ##contig=<ID=cneoH99_Chr5,length=1814975> ##contig=<ID=cneoH99_Chr6,length=1422463> ##contig=<ID=cneoH99_Chr7,length=1399503> ##contig=<ID=cneoH99_Chr8,length=1398693> ##contig=<ID=cneoH99_Chr9,length=1186808> ##contig=<ID=cneoH99_Chr10,length=1059964> ##contig=<ID=cneoH99_Chr11,length=1561994> ##contig=<ID=cneoH99_Chr12,length=774062> ##contig=<ID=cneoH99_Chr13,length=756744> ##contig=<ID=cneoH99_Chr14,length=926563> ##phasing=none ##commandline="freebayes --region cneoH99_Chr9:0..1186808 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_cneoH99_Chr9:0..1186808.vcf" ##filter="DP > 10" ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record."> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=DPR,Number=A,Type=Integer,Description="Number of observation for each allele"> ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown cneoH99_Chr1 99 . T C 50426.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1415;CIGAR=1X;DP=1415;DPB=1415;DPRA=0;EPP=6.6949;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.983;MQMR=0;NS=1;NUMALT=1;ODDS=1966.21;PAIRED=0.928622;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=56243;QR=0;RO=0;RPL=619;RPP=51.0881;RPPR=0;RPR=796;RUN=1;SAF=781;SAP=36.1717;SAR=634;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1415:1415,1415:0:0:1415:56243:-5056.15,-425.957,0 cneoH99_Chr1 161 . C G 52460.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1487;CIGAR=1X;DP=1487;DPB=1487;DPRA=0;EPP=21.0027;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=2066.02;PAIRED=0.958978;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58459;QR=0;RO=0;RPL=795;RPP=18.5027;RPPR=0;RPR=692;RUN=1;SAF=787;SAP=14.0633;SAR=700;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:DPR:RO:QR:AO:QA:GL 1/1:1487:1487,1487:0:0:1487:58459:-5255.54,-447.632,0 cneoH99_Chr1 168 . T C 53275.2 . Nnadi Nnaemeka Emmanuel Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

…

On Tue, Jan 9, 2018 at 8:20 PM, TAB Walsh ***@***.***> wrote: In response to your questions: 1. Actually, mp_prep.py will accept any number of VCF files, and will extract genotype data only for the specified pool sample and its two parent samples. So you could pass one VCF file containing the pool and parent samples, one VCF containing the pooled sample and one containing both parent samples, or even a separate VCF file for each sample. All of these would be valid input. 2. The VCF file input to mp_prep.py can contain data for both high and low samples, but you would need to set parameter -p (the pool sample name) of either the high pool or the low pool. Each call to mp_prep.py script produces a single allele count file containing data for a single pool, which can then be input to the main Multipool script ( mp_inference.py). If you have both a high and low pool, you will need to run mp_prep.py once for each pool, then input both allele count files simultaneously to mp_inference.py. 3. The text string in the rightmost column of the top row of your VCF excerpt, above the sample genotype data, is the sample name. In this example it is unknown, but it could just as easily be High_Pool, for example. In response to the error, parameters -p and -f should be the names of the pool sample and founder samples, respectively. Please have a look at the help output for this script, which can be viewed with the following command: python2 mp_prep.py -h Before running this prep script, you will need to check the VCF data to find the names of the pool samples and the founder samples. These must then be specified when you run the script, so that it knows which samples are which. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/matted/multipool/issues/10#issuecomment-356386267>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Aeq25-GNs91aVRUzz9jCqOgdDMoRvkGqks5tI7v6gaJpZM4RWpA2> .

[emmannaemeka]

@tw164 Please how can i resolve this
Input variant file(s): /Users/emmannaemeka/Desktop/QTLT/Parents.vcf:/Users/emmannaemeka/Desktop/QTLT/Pool.vcf
Pool sample: Trimmomatic_on_Low_bulk_R
Founder sample(s): Trimmomatic_on_KN99a_R,Trimmomatic_on_EN28
Region(s): cneoH99_Chr1
Output allele depth file: allele_counts.txt
Checking for pool and founder samples in input variant data...
Sample 'Trimmomatic_on_KN99a_R' found in input file(s): /Users/emmannaemeka/Desktop/QTLT/Pool.vcf
Sample 'Trimmomatic_on_EN28' found in input file(s): /Users/emmannaemeka/Desktop/QTLT/Pool.vcf
Sample 'Trimmomatic_on_Low_bulk_R' found in input file(s): /Users/emmannaemeka/Desktop/QTLT/Parents.vcf
Getting founder allele info...
[W::vcf_parse] Contig 'cneoH99_Chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'cneoH99_Chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
Found 9 variants in region 'cneoH99_Chr1' of founders 'Trimmomatic_on_KN99a_R' and 'Trimmomatic_on_EN28'...
Of these, 8 are SNPs...
Of these, 0 have homozygous genotypes...
Of these, 0 are segregating with respect to founders 'Trimmomatic_on_KN99a_R' and 'Trimmomatic_on_EN28'...
Traceback (most recent call last):
File "mp_prep.py", line 490, in
sample_file_info, quiet=quiet)
File "mp_prep.py", line 361, in get_founder_allele_info
"for region '{}'".format(region))
RuntimeError: founder alleles not found for region 'cneoH99_Chr1'

[tw164]

@emmannaemeka All sample names are in the header line of the VCF file. (See here for an introduction to the VCF format, and here for the VCF format specification.)

You can view the header line with the following bash command:

grep "^#[^#]" file.vcf

If you have bcftools installed, you can view a list of samples as follows:

bcftools query --list-samples file.vcf

Without knowing more about your data, I can only guess at the reason, but the RuntimeError appears to be due to a lack of SNP data for the reference sequence "cneoH99_Chr1".

[emmannaemeka]

I have found away around the problem. It worked. I have attached the plot of one of the chromosomes. Can you assist in interpreting it?

[tw164]

@emmannaemeka This output is a little different from that of the original version of Multipool in that the LOD curve is shown in black, and individual data points are not displayed. However, in most respects the output is broadly similar to the original Multipool, and so the Multipool wiki provides the best general guidance to interpreting Multipool output.

For more specific assistance, you would need to provide more information about the input data and parameters used. For example, what species are the samples taken from? What is the phenotype being tested? What reference genome (or genomes) did you use when calling SNPs? How many SNPs did you find in each sample, particularly on the chromosome shown in the plot above? What were the commands used for running mp_prep.py on each pool? And what parameter settings did you use when running mp_inference.py?