The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
StrandBiasbySample, FisherStrand Annotation
Hi, I am using GATK version 3.2-2 to analyze miseq data from a human snp panel, aligned to it's "own" reference. I use unifiedgenotyper to call all desired SNPs (ref or non-ref variants) from the panel and it works very well. I would like to know reverse and forward reads for each allele. I have used FisherStrand values, but they are all 0.00, meaning there is no strand bias ? I assume strandbias SB or StrandBiasBySample are not used anymore ? Is there any other way I can get forward and reverse reads without having to walk through the bam file ?