Question: Fisher Strand in GATK, a good measure to detect Strand Bias?
1
gravatar for cristianrohr768
3.8 years ago by
Spain
cristianrohr76830 wrote:

Hello,

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?

 

 

 

 

fisher strand strand bias gatk • 2.5k views
ADD COMMENTlink modified 3.8 years ago by Zaag720 • written 3.8 years ago by cristianrohr76830
1
gravatar for Zaag
3.8 years ago by
Zaag720
Amsterdam
Zaag720 wrote:

It tests the difference between variant and ref alleles so probably the ref alleles on that position are also on the forward strand, so the bias is the same for ref and var reads so there is no reason there to discard the variant.

ADD COMMENTlink written 3.8 years ago by Zaag720
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