This workflow represents the GATK Best Practices for SNP and INDEL calling on RNA-Seq data.
Starting from an unmapped BAM file, it performs alignment to the reference genome, followed by marking duplicates, reassigning mapping qualities, base recalibration, variant calling and variant filtering. On the GATK website, you can find more detailed information about calling variants in RNA-Seq.
Common Use Cases
- If y
This is a companion discussion topic for the original entry at github.com/sevenbridges-openworkflows/Broad-Best-Practice-rnaseq-germline-snps-indels-CWL1.0-workflow