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

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

       -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/>