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Question for FisherStrand
I am trying to interpret the FisherStrand provided by GATK variant annotation.
By using variant annotation tools in GATK, I made the vcf files annotated with FisherStrand.
For my detected mutation predictions (about 1100 nonsynonymous mutations in WES), I want to check their strands and remove if the mutations contain the reads with strand bias.
In documentations, I found some information as follows :
1) the higher the output value, the more likely there is to be bias.
2) FisherStrand is best suited for low coverage situations. For testing strand bias in higher coverage situations, see the StrandOddsRatio annotation.
From this points, my questions are that
1) It is obvious that mutations annotated with low output value in FisherStrand, it has no strand bias..therefore I will remove the mutations with higher FS scores. However, I couldn't determine the value of threshold for FisherStrand. the values are very vary according to each mutation. Therefore do you have any suggested threshold value for FisherStrand so that I remove the real strand biased mutation?
2) I used the whole exome sequencing data which have coverage depth of >90X on average. So FisherStrand is also suitable for my data?
Or I use other library to check the strand ratio for the accuracy? (But, I want to use FisherStrand because I already made the output by taking my a lot of time!!)
I look forward to your helpful comments.