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 zst
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.
- -distrreg
- distribute regions for parallel processing. Possible options
are 0: no distribution (also empty) 1: default
distribution schr or schromosome: each chromosome processed
separately chr or chromosome: each chromosome processed
separately, except the unsorted, etc. with a _ in the name that
will be combined), a number: distribution into regions of this
size a number preceded by an s: distribution into regions
targeting the given size, but breaks can only occur in unsequenced
regions of the genome (N stretches) a number preceded by an r:
distribution into regions targeting the given size, but breaks can
only occur in large (>=100000 bases) repeat regions a
number preceded by an g: distribution into regions targeting the
given size, but breaks can only occur in large (>=200000 bases)
regions without known genes a file name: the regions in the
file will be used for distribution
- -refseq refseq
- The -distrreg option requires a genome reference sequence,
which must be given using this option
- -skip skipfile
- Do not run if skipfile exists
Category
Format Conversion