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