Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Specify more than one snpmask with Fasta Alternate Reference Maker
I am hoping to use multiple snpmask vcfs with fasta alternate reference maker. The description of fasta alternate reference maker says "...it allows for one or more "snpmask" VCFs to set overlapping bases to 'N'."
However, I haven't been able to figure out how to specify multiple snpmasks.
I have tried
--snpmask mask1.vcf mask2.vcf
--snpmask mask1.vcf --snpmask mask2.vcf
but both give the error:
Argument 'snpmask' has too many values.
Both mask1.vcf and mask2.vcf work fine on their own (when only one snpmask specified).
I am using GATK v3.8-0.
My apologies for this very basic question! I've read the documentation carefully and searched for "--snpmask" in the forums, but am still stuck - any pointers would be appreciated!