multiple vcf files in FastaAlternateReferenceMaker
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.
Hi Tiffany, thank you for your reply. I ended up using gatk CombineVariants to merge the vcfs (before posting this, just wanted to see if there was a way to do this using FastaAlternateReferenceMaker)
Is there a difference between CombineVariants and MergeVcfs?
No problem! CombineVariants is not in GATK4 and hasn't been ported over because it's got to be fixed up. MergeVCFs is meant to do the same thing. That being said, if your files were merged correctly using the older tool, I think you are good to go.
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