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, --min-MQ INT
              Only count reads with mapping quality greater than or equal to 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.

       -c     Print an additional column with the read count for this region.  This  will  be  +1
              for  every  read  covering the region, not just starting within in.  The whole read
              filtering options -Q, -g and -G options will also have an affect on this count, but
              -d will not.

       -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/>