I follow the GATK good practices to call variants on 11 samples from a custom truseq design. I do Joint genotyping and apply Hard Filters to my data http://gatkforums.broadinstitute.org/discussion/2806/howto-apply-hard-filters-to-a-call-set.
In a second test, i skip the joint genotyping step, and just apply hard filters to my individuals VCFs.
With boot strategies i found the same variant in the same individual wich is a pathogenic variant for a disease i was interested in.
For this variant i have a read depth of 180, and i see A:103 and G:77, G is the reference, there aren't homopolymers near. But the problem is that this position is ONLY covered by forward reads.
The FS calculated by GATK for this position is FS=0.000
FS is Phred-scaled p-value using Fisher’s Exact Test to detect strand bias (the variation being seen on only the forward or only the reverse strand) in the reads. More bias is indicative of false positive calls.
So a value of 0 must be indicative of no bias, but this position is only covered by forward reads, so i undoubtedly had strand bias in this position.
So what's going on?? i can have confidence on this variant?