To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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

ihleeihlee Member
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


  • ebanksebanks Broad InstituteMember, Broadie, Dev

    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).

  • 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 InstituteMember, Broadie, Dev

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

Sign In or Register to comment.