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)
  -v                    prints program version
  --output-strands      outputs coverage and stats separately for each strand
  --format=CHOICE       output format

Usage examples:

• Detect low-coverage regions

Split coverage by read strand

When the target enrichment is performed with highly-multiplexed PCRs (e.g. MIPs) one could be interested in checking if a region is only covered by forward or reverse reads. To allow this check, covtobed --output-strands will print two separate coverage columns:

covtobed  --output-strands test/mp.bam 

The output will print the coverage from forward reads in the 4th column, and coverage from reverse reads in the 5th column. The following example shows a strand bias at the beginning and the end of a chromosome:

NC_001416.1	0	2	0	0
NC_001416.1	2	13	0	1
NC_001416.1	13	14	0	2
NC_001416.1	14	18	0	3
NC_001416.1	18	21	0	4
NC_001416.1	21	31	0	5
[...]
NC_001416.1	2767	2772	5	0
NC_001416.1	2772	2774	4	0
NC_001416.1	2774	2778	3	0
NC_001416.1	2778	2796	1	0