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Test-drive the GATK tools and Best Practices pipelines on Terra
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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 ?