a situation that three variants of EGFR exon19 deletion can't be merged to one

[ShannonDaddy]

Hi, as the images shows, I have three variants with almost same frequencies that should merged togther, I use vargroup.py for that, It turns out that only the first and third variants were merged, the second one was rejected. I can't figure out the reason. can you check that for me. My command shell script, bam file, vcf file, grouped vcf file are archived and attached.

Thanks a lot!
T438267.zip

[alliemclean]

I am trying to debug but the sample numbers for the vcf and bam are different in the attached zip.

T403764.flt.vcf
T438267.bam

It looks like the bam is the correct one. Could you double check the vcf?

[ShannonDaddy]

I am trying to debug but the sample numbers for the vcf and bam are different in the attached zip.

T403764.flt.vcf
T438267.bam

It looks like the bam is the correct one. Could you double check the vcf?

sorry, my fault, i reupload the zip file, please check it out, thanks!
T438267.zip

[alliemclean]

Thanks! The vcf still wasn't right but I was able to reproduce the error by adding the correct variants. It seems that there's an error calculating positions if there are insertions and deletions. I submitted a PR for this but I no longer have write access to this repo. Tagging @hackermd.