The documentation here https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker states that for input:
The reference, requested intervals, and any number of variant files.
My question is, how to provide more than one variant file?
I tried using
-V snps.vcf -V indels.vcf
however it complains "Argument '[V, variant]' cannot be specified more than once."
-V snps.vcf indels.vcf
but no luck. I tried scouring the web, also no luck.
Please sign in to leave a comment.