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Which bundle should I use for bam files from Illumina's CASAVA pipeline?

ihleeihlee Posts: 2Member
edited January 2013 in Ask the GATK team

I have bam files generated by Illumina's CASAVA pipeline, and the reference genome version in the accompanying document is 'NCBI37_UCSC'. The chromosomes are all named after UCSC hg19 convention, but 'NCBI37' part in the name confuses me. I'm not sure which bundle files should I use with these bam files, b37 or hg19.

Post edited by Geraldine_VdAuwera on
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Answers

  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Developer, Broadie, Moderator, DSDE Member, GP Member admin

    You should ask Illumina as they provided these files for you. You need to make sure that Illumina used a standard reference - and if not then they need to provide you with the necessary reference file(s).

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • ihleeihlee Posts: 2Member

    The reference files did come with the bam files. I'm just not sure whether they're from NCBI build or UCSC build. I hoped someone with much experience in handling Illumina data with GATK might help me to solve this problem.

  • ebanksebanks Broad InstitutePosts: 684Member, Administrator, GATK Developer, Broadie, Moderator, DSDE Member, GP Member admin

    You should post in the Ask The Community section then. I've just moved this discussion there.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

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