SNV annotation files are missing

[FL512]

Hi Daniela,

It's Ken, I have posted my issule "Analyzed bams uder subdirectly" on May 17, 2023.
Thank you again for your help at that time.

Unfortunately, I had to involve other project right after and I did not have any time to work on my mitochondria research.
Finallay, I am back. I have restarted all analyses.

My question today is that I got noticed that there were no SNV annotation files generated after the run.
I tried both ways according to your instruction (RUN PIPELINE SECTION).
$HP_SDIR/run.sh > run.all.sh
bash ./run.all.sh

and
grep filter.sh ./run.all.sh | parallel ; getSummary.sh

Except SNV annotation files, I think all are generated properly because I have count.tab, cvg.tab and so on for each samples and for the summary files.

I have downloaded and installed MitoHPC onto our computer workstation a year ago with the help of IT guys because I cannot deal with any WGS data on my local PC nor PCs that are connected to the Internet due to security reasons in my institute.

Anyway, can you please give me a comment or suggestion regarding this issue?
Or do you think I need to re-install the latest version of mitoHPC to fix this problem?

Thank you very much!
Ken

[dpuiu]

Hi Ken,

Did you have a look at the VCF files under each sample directory to make sure they are not empty?

That could happen if your reads are either unmated, have very low coverage, or low quality.

For the example2/sample_A that comes along with MitoHPC, you can check as follows:

$ grep -c ^c examples2/out/sample_A/sample_A.*.00.vcf
examples2/out/sample_A/sample_A.mutect2.00.vcf:74
examples2/out/sample_A/sample_A.mutect2.mutect2.00.vcf:74

If the VCF files are fine, you can try rerunning getSummary.sh.