MuTect2: multiple dbsnp files issue

Hi,
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?

Thanks,
Parthav

Answers

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