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From: Ryan G. <gol...@um...> - 2011-04-26 14:33:58
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Hi - I've noticed that when sorting BAM files with samtools, the chromosomes are sorted lexicographically. GATK insists on the chromosomes being sorted numerically. I'm using Picard tools right now to make the conversion. I thought, at first, the sorting was based on the order of the chromosomes in my fasta file when I indexed the genome, but that doesn't seem to matter. Is there a way to have samtools sort the chromosomes numerically or match the order in the .fai file? This could help eliminate a step that currently takes some time to run, perhaps as an option to the sort command? |