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/>

samtools-1.10                                    6 December 2019                              samtools-bedcov(1)