default options excluding entries with PASS filter? about vcf2tsvpy HOT 5 CLOSED

Hey @BCArg, thanks for looking into this. One might of course considering implementing some warnings when encountering data like you have, but this is really unexpected input, I believe. Sadly, my experience is that VCFs from different callers rarely adhere strictly to the VCF specification, which makes it inherently difficult to cope with all scenarios. If you have not done so already, you might want to check out the vcf-validator, to get some feel for how "valid" your VCF file is.

from vcf2tsvpy.

having a closer look at the entries that were removed, I see that they have GQ (genotype quality 0), so I guess this is the reason.

from vcf2tsvpy.

I just noticed the same now. Wonder how these could be annotated as PASS?

from vcf2tsvpy.

They also have an undefined genotype (GT).

from vcf2tsvpy.

That's correct, GT is always './.', from the entries that I checked. Indeed it is a bit dodgy that they are annotated as PASS, but other quality parameters are poor. Anyway, I reckon your tool is performing as expected, so I will close this issue, thanks for the assistance

from vcf2tsvpy.