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What resource data files are needed for running MuTect?

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
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 uses the following resources:

Post edited by Geraldine_VdAuwera on


  • Hi, I am getting incompatible contig error while trying to use these vcf files. Apparently the vcf input files have 1-22, X, Y, MT; while both my reference genome and BAM files have the following. How can I run MuTect on my BAM files?

    chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Please see the GATK FAQs about genome reference files.

  • GumiltonGumilton United StatesMember

    I have downloaded dbsnp_138.hg19.vcf from the bundle. May I use this dbsnp_138.hg19.vcf for MuTect instead of dbsnp_132_b37.leftAligned.vcf.gz you mentioned? Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That should be fine, @Gumilton; just make sure you're using either all b37 resources or all hg19, otherwise you'll run into compatibility problems.

  • GumiltonGumilton United StatesMember

    @Geraldine_VdAuwera Thank you! In terms of genome version, I am using hg19... So I will use dbsnp of hg19 in my system. How about the cosmic file? b37_cosmic_v54_120711.vcf? You mentioned this is renamed from hg19. May I assume they have the same content with just different file name? So am I safe to use this file b37_cosmic_v54_120711.vcf you mentioned in my pipeline where all other files are all hg19? Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I think that should be fine, yes.

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