Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

accessory scripts for processing varscan somatic/copynumber outputs.

Pipeline of somatic variant analysis using Waldenstrom macroglobulinemia patient’s RNA-seq data, including tools like STAR, HTseq, VarScan in parallel computing in SGE clusters, Deseq2 and GSEA in R

GATK and VARSCAN analysis pipeline

Convert VarScan output to VCF format

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

varscan repo contains code for Varscan workflow