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# In my VCF, what specifically does the filter Indel_FS mean?

Member
edited January 2013

I am filtering looking for rare variants and found some frameshift variants in an interesting gene. Some of them are noted as PASS in the QC column of the VCF and some are noted as Indel_FS . What exactly does that second notation mean? I am almost positive that these will validate given how they segregate in my subjects.

Post edited by Geraldine_VdAuwera on
Tagged:

• Member, Dev

There are no standard filters in VCF, they're described in the meta-information lines of each file (see the spec: http://www.1000genomes.org/wiki/Analysis/Variant Call Format/vcf-variant-call-format-version-41).

If I had named that filter, it would be for Indel calls that fall outside some threshold on the FS metric - exactly what the threshold is should be defined in the meta-info.

• Member

Thanks.
Andrew

• Member, Dev

It's also defined in the meta-information, it's a measure of strand bias. There's documentation on this site (Guide/Technical Documentation/VariantAnnotator Annotations/FisherStrand), but it's pretty brief. If you really want to understand it, check out the source.