Combine Variants on numerous vcf
Hi GATK team,
Is there a way to use CombineVariants on multiple vcf files, without retyping the "-V A.vcf -V B.vcf -V C.vcf etc." for each and every vcf file?
we usually have 50-100 vcfs to combine, so this is not a feasible option
Your DepthOfCoverage walker has the function I'm looking for, as multiple bams can be passed as a single file holding the names of the bam files to analyze, eg. "-I bamnames.list".
However, a similar function appears to be missing in CombineVariants, which makes this walker very difficult to use in if you have many vcfs to combine.
Thanks for a great toolkit!