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United StatesMember Posts: 10
edited September 2013

Hello,

I have the following variant called by Unified Genotyper (GATK version : GenomeAnalysisTK-2.6-5) :

The FS score is 37.414. But a closer look at the bam file indicates that the 115 reads supporting alternate allele G are all in + strand. Shouldn't the FS score be much higher for this variant? 113 reads reads supporting the reference allele T at this position are in + strand and 67 are in - strand.

Tagged:

Hmm, at first glance I would also expect a higher FS value. Can you tell me if this data has been compressed with ReduceReads, by any chance?

Geraldine Van der Auwera, PhD

• United StatesMember Posts: 10

Hi Geraldine,

My pipeline includes: Novoalign -> PICARD (mark and remove duplicates) -> GATK.

OK, just checking. RR has had a few bugs that caused annotation weirdness before.

Here's a way to test what might be going on here. We recently added a new annotation (StrandBiasBySample) that is just the counts of the bases going into the FS calculation.  Could you use the Variant Annotator (with -A StrandBiasBySample) with the latest nightly build on your VCF at this one site? Then post the result here for us?

Geraldine Van der Auwera, PhD

• United StatesMember Posts: 10

Hi Geraldine,

Sure. I will try that and let you know.