I have WES data of tumor samples with matched ones extracted from 13 patients (paired-end, illumina). I used BWA mem to align them against hg38, and used VarScan2 to call somatic variations. Now I have 6 files (fpfilter_Passed.vcf) for each patient (Somatic, LOH, Germline for each of snp and indel variations).
I am trying to merge the vcf files of each patient using CombineVariants and MergeVcfs (Picard) of gatk, but no success yet. Can any one tell me if I am on the right way? Is there any other tools that I can try?
Thanks for any help!