Quantifying the expression of SNVS & RNA-seq reads
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beginner984 commented
Sorry,
This is not any issue with GATK indeed, rather my confusion;
I have been given a bunch of .bam files (marked duplicates) from STAR aligner; Likely I will need "Calling variants in RNAseq"
Sorry, please say I should find Reads overlapping any SNV using the ReadCountWalker in gatktools
I can not find any tutorial, related discussion, ..
Any help please? For workflow, getting intuition
Thank you, I look forward to hearing from you