NAME

       samtools-bedcov - reports coverage over regions in a supplied BED file

SYNOPSIS

       samtools bedcov [options] region.bed in1.sam|in1.bam|in1.cram[...]

DESCRIPTION

       Reports  the  total  read  base  count  (i.e.  the  sum  of per base read depths) for each genomic region
       specified in the supplied BED file. The regions are output as  they  appear  in  the  BED  file  and  are
       0-based.  Counts for each alignment file supplied are reported in separate columns.

OPTIONS

       -Q INT Only count reads with mapping quality greater than INT

       -g FLAGS
              By  default, reads that have any of the flags UNMAP, SECONDARY, QCFAIL, or DUP set are skipped. To
              include these reads back in the analysis, use this option together with the desired flag  or  flag
              combination.  FLAGS can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal
              by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-
              separated list of flag names. [0]

              For a list of flag names see samtools-flags(1).

       -G FLAGS
              Discard any read that has any of the flags specified by FLAGS set.  FLAGS are specified as for the
              -g option. [UNMAP,SECONDARY,QCFAIL,DUP]

       -j     Do not include deletions (D) and ref skips (N) in bedcov computation.

       -d INT Print an additional column, for each file, containing the number of bases having a depth above and
              including  the  given threshold. If the option is not used, the extra column is not displayed. The
              option value must be an integer >= 0.

       -X     If this option is set, it will allows user to specify customized index  file  location(s)  if  the
              data  folder does not contain any index file. Example usage: samtools bedcov [options] -X <in.bed>
              </data_folder/in1.bam> [...] </index_folder/index1.bai> [...]

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1)

       Samtools website: <http://www.htslib.org/>