Using covtobed

Synopsis

Usage: covtobed [options] [BAM]...

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
                        (default: 0)
  --output-strands      outputs coverage and stats separately for each strand
  --format=CHOICE       output format

Usage examples:

• Detect low-coverage regions
• Check coverage by strand
• Calculate the physical coverage
• Alternative output: "counts"