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.
MuTect2: multiple dbsnp files issue
I have used MuTect versions earlier than MuTect2, and I have successfully provided two dbsnp files in the mutect call (I am working with mouse, and its a mixed strain with two parental backgrounds. So I would like to provide germline SNPs for both strains).
However, when I tried the same with MuTect2 using two dbsnp files (--dbsnp 1.vcf --dbsnp 2.vcf), it threw an error indicating that more than one dbsnp files are not permitted.
Is this a change going from Mutect1 to Mutect2 that only one dbSNP file can be provided?