covtobed1
Convert the coverage track from a bam file into a bed file
Usage
covtobed [options]
[BAM] ...
Overview
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