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multiple vcf input to SelectVariants
I am trying to use the GATK (3.6) SelectVariants tool, and I want to input several vcf files. Preferably all as --variant (-V). The key here is that these have to be separate files, not one multi sample VCF. Supposedly SelectVariants can take a list of vcf files, but it is unclear (to me) how. I tried -V input1.vcf -V input2.vcf ... and -V input1.vcf input2.vcf ... and both throw an error. So how exactly can I provide a list of vcf files? Alternatively, which tool to use to select variants from multiple vcf files (I do not want to use the --concordant option because in some cases I want to select variants present in a fraction of input files, and I do not care much in which specific file given variant shows up). I'm grateful for any hints! Thanks!