Hi
I have some questions about GATK, I hope to someone can help me :)
What is the Fisher exact test to calculate the Strand Biase in GATK? is weight or no? I haven't see any documentation about the statistical calculation.
Other questions, Is possible to obtain the number of Forwards reads and Reverse reads in a variation position?
Thank You very much
Best REgards
good to know. you mean FS > 60 as a genome-wide cutoff? might want a smaller one for a subset or selected region.
You may be right. I got these values from GATK web site and have seen few papers using it but I have no idea how they came up with these thresholds. When I use samtools that gives you the p-value for the strand bias, I remove variants with strand bias < .0001 and I assume that translates a Phred score of 40. so a smaller value should make more sense.