Generate realistic human genome

[anushishah]

Hi,
I am trying to generate realistic human genome by following link : https://htmlpreview.github.io/?https://raw.githubusercontent.com/sequencing/EAGLE/master/doc/html/EAGLE%2BUse%2BCase%2B-%2B2x250%2Brealistic%2BHuman%2Bsequencing%2Bsimulation.html

Could you please provide information about meta-data for MotifQualityDropTables, TemplateLengthTables and QualityTables?

Essentially I want to generate realistic human genome with some error rate. Could you please advise parameter(s) for that?

Thanks very much !

[janinl]

Oops I need to update those paths indeed.
In the meantime, here are the locations of those files in this git repo:

• MotifQualityDropTables: https://github.com/sequencing/EAGLE/blob/master/data/MotifQualityDropTables/DefaultMotifQualityDropTable.tsv
• TemplateLengthTables: https://github.com/sequencing/EAGLE/blob/master/data/TemplateLengthTables/TemplateLengthTableFrom2x250Run.tsv
• QualityTables:
  • https://github.com/sequencing/EAGLE/blob/master/data/QualityTables/NewQualityTable.read1.length251.qtable2
  • https://github.com/sequencing/EAGLE/blob/master/data/QualityTables/NewQualityTable.read2.length251.qtable2

[anushishah]

Thank you janinl for providing the location of the files. Appreciate that!

Would it be please possible to know what data inside the files means? Also, what aspects of realistic genome generation they are associated with?

[anushishah]

Hi @janinl ,

Would the realistic genome simulated also contain false positive variants?

I am trying to generate realistic genome for Chr 22 using following command (below). Here, I don't introduce any variant (None.vcf). And the output BAM file also doesn't pick any variant by running GATK variant caller. However, I would expect some false positive variants being introduced. Any idea why would that be the case, any suggestions to tweak parameters?

EAGLE_SHARE=/usr/local/share/EAGLE

configureEAGLE.pl
--run-info=$EAGLE_SHARE/RunInfo/RunInfo_PairedReads2x251Cycles2x64Tiles.xml
--reference-genome=/Genomes/hg38/Chromosomes/
--variant-list=$EAGLE_SHARE/Variants/None.vcf
--coverage-depth=30
--genome-mutator-options="--organism-ploidy=2 --ploidy-chromosome=chrX --ploidy-level=1 --ploidy-chromosome=chrY --ploidy-level=1 --ploidy-chromosome=chrM --ploidy-level=100"
--motif-quality-drop-table=$EAGLE_SHARE/MotifQualityDropTables/DefaultMotifQualityDropTable.tsv
--template-length-table=$EAGLE_SHARE/TemplateLengthTables/TemplateLengthTableFrom2x250Run.tsv
--quality-table=$EAGLE_SHARE/QualityTables/NewQualityTable.read1.length251.qtable2
--quality-table=$EAGLE_SHARE/QualityTables/NewQualityTable.read2.length251.qtable2

cd EAGLE
make -j 4
make bam