Which bundle should I use for bam files from Illumina's CASAVA pipeline?
Posted in Ask the GATK team | Last updated on 2013-01-07 20:07:55


Comments (3)

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.


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