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Bam files for MuTect

Are the requirements for the BAM files the same for MuTect as for GATK.
I have the tumor and normal bam files and they are co-ordinate sorted, indexed and aligned to MM9 using TopHat.
I have the snp vcf file as well as the reference fasta file in order. But, When i run muTect I get an error saying BAM files are not indexed. Can anyone help suggest me what should I try next?.
Thanks,
Himanshu

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The indexing requirement is the same for MuTect as for GATK. Your bam files each need to have a *.bai index file that matches the name of the bam file.

  • hns04hns04 Member

    Hi Geraldine,
    Thanks a lot for your reply.
    I do have the bai file with the same name as the bam file. Also, i have the read group header and they are co ordinate sorted.
    What could be going wrong?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm, that's odd. Can you post the error message?

  • hns04hns04 Member

    Thanks Geraldine,
    The error message is as follows.

    ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.

    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm. Well, maybe the index file is corrupted. Try generating the index file again (eg with Picard), not much else to do at this point.

  • noanoa Boston areaMember

    Hi,
    I receive the same error message when calling RealignerTargetCreator although I have the .bai files. I generated them with samtools index and then tried also picard but still getting the same error, do you have any suggestions?
    Thanks,
    Noa
    I'm using version 2014.4-3.3.0-0-ga3711aa

    ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.

  • noanoa Boston areaMember

    Please ignore my message, I found my mistake and it works now. Thanks

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