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