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What genome builds does MuTect support?

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited December 2015 in MuTect v1 Documentation

Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to call both SNPs and indels. See the GATK version 3.5 release notes and the MuTect2 tool documentation for further details.

MuTect is technically capable of processing any genome build you want, including genomes of non-human organisms. However, we currently only provide explicit user support for the following genomes: Human (hg18, hg19, b37) and Mouse (mm9). In time we will expand this to other genome builds.

Human hg18

-R Homo_sapiens_assembly18.fasta
--dbsnp dbsnp_132.hg18.vcf
--cosmic hg18_cosmic_v54_120711.vcf

Human hg19 / b37 (GRC37)

-R Homo_sapiens_assembly19.fasta
--dbsnp dbsnp_132_b37.leftAligned.vcf
--cosmic hg19_cosmic_v54_120711.vcf

Mouse mm9

-R Mus_musculus_assembly9.fasta
--dbsnp dbsnp_128_mm9.vcf

There is no cosmic VCF available for mouse, so that parameter can be eliminated entirely

Post edited by Geraldine_VdAuwera on
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