NAME
covtobed - convert the coverage track from a BAM file into a BED file
SYNOPSIS
covtobed [options] [BAM]...
DESCRIPTION
Computes coverage from alignments
OPTIONS
- -h, --help
-
show this help message and exit
- --version
-
show program's version number and exit
- --physical-coverage
-
compute physical coverage (needs paired alignments in input)
- -q MINQ, --min-mapq=MINQ
-
skip alignments whose mapping quality is less than MINQ (default: 0)
- -m MINCOV, --min-cov=MINCOV
-
print BED feature only if the coverage is bigger than (or equal to) MINCOV (default: 0)
- -x MAXCOV, --max-cov=MAXCOV
-
print BED feature only if the coverage is lower than MAXCOV (default: 100000)
- -l MINLEN, --min-len=MINLEN
-
print BED feature only if its length is bigger (or equal to) than MINLELN (default: 1)
- -d, --discard-invalid-alignments
-
skip duplicates, failed QC, and non primary alignment, minq>0 (or user-defined if higher) (default: 0)
- --output-strands
-
output coverage and stats separately for each strand
- --format=CHOICE
-
output format