Missing ID and filter column in a vcf file

Question

[Chris]

Hi all, I created a vcf file using samtools and bcftools but it missed ID and filter column like this, just a dot. So there is something wrong in the process or it is normal? Don't know how to make the photo bigger in this case. Thank you so much.

Answer 1

[iraun]

Hi! If I recall it properly, a dot in the FILTER field of samtools VCF indicates that the variant is of good quality and that all the filters have passed (if not, the FILTER field would indicate the name of the filter that the variant has not passed). Regarding the ID field, usually you can get an ID after annotating the variants downstream using tools such as VEP or snpeff. If the variant is a known polymorphism for example, after annotating the VCF using dbsnp as database, the variant will get an ID starting with rs prefix.

[Chris]

Got it. Thank you! I looked at other vcf file and it wrote PASS under filter column so I am not sure.

[iraun]

Yes, that is true. Usually most variant calling tools label the variants as PASS when the variant passes all the filters. Not sure exactly how samtools behaves. Have you checked if you have variants labelled as PASS? If so, then it must be other explanation for the dot. I am a bit suspicious that those variants you posted are good... the QUAL field is quite low to be a PASS, so maybe a dot means something else after all :/. FYI, just read in here that a dot in FILTER column for bcftools means that FILTER is not set.

[Chris]

I don't see PASS in my vcf file. Only this in the first two lines of my vcf file:

fileformat=VCFv4.2
FILTER=<ID=PASS,Description="All filters passed">

So dot that means I haven't filter variants based on quality score yet? Thank you!