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?