Bam2sam
Format
cg bam2sam ?options? bamfile ?samfile?
Summary
convert bam (or cram) to sam, sorting chromosomes into natural
sort order.
Description
Arguments
- bamfile
- bam file to analyse
- samfile
- resultfile, if not given or -, send results to stdout
Options
- -sortchr 0/1
- default 1 sorts chromosomes in output to natural sort (used
in most genomecomb tools) if 0, the sort does not happen, and
bam2sam simply calls samtools view to do the conversion
Category
Format Conversion