Genomecomb moved to github on https://github.com/derijkp/genomecomb
with documentation on https://derijkp.github.io/genomecomb.
For up to date versions, go there. These pages only remain here for the data on the older scientific
application (or if someone really needs a long obsolete version of the software)
Bam2reg
Format
cg bam2reg ?options? bamfile ?mincoverage? ?outfile?
Summary
Extract regions with a minimum coverage from a bam file.
Description
Arguments
- bamfile
- bam file to analyse
- mincoverage
- minimum coverage
- outfile
- result file containing the regions with coverage >=
mincoverage. If not given, a filename of the form
sreg-cov<mincoverage>-<bamfilerootname>.tsv will be
used. If the -compress 1 option is given, it will be compressed
using lz4
Options
- -mincoverage mincoverage
- mincoverage given as an option instead of a parameter
- -compress 0/1
- Compress the output file (or not) if no outfile is given. If
outfile is given, the extension of the file name will determine
compression.
- -skip skipfile
- Do not run if skipfile exists
Category
Format Conversion
