Man page - covtobed(1)

Packages contains this manual

Package: covtobed
apt-get install covtobed

Manuals in package:

Documentations in package:

covtobed - convert the coverage track from a BAM file into a BED file

covtobed [ options ] [ BAM ]...

Computes coverage from alignments

-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