NAME

       samtools depth - computes the read depth at each position or region

SYNOPSIS

       samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]]

DESCRIPTION

       Computes the depth at each position or region.

OPTIONS

       -a      Output all positions (including those with zero depth)

       -a -a, -aa
               Output  absolutely all positions, including unused reference sequences.  Note that
               when used in conjunction with a BED file the -a option may sometimes operate as if
               -aa  was  specified  if  the reference sequence has coverage outside of the region
               specified in the BED file.

       -b FILE Compute depth at list of positions or regions in specified BED FILE.  []

       -f FILE Use the BAM files specified in the FILE (a file of filenames, one file  per  line)
               []

       -H      Write  a  comment  line  showing column names at the beginning of the output.  The
               names are CHROM, POS, and then the input file name for each depth column.  If  one
               of  the  inputs  came  from stdin, the name “-” will be used for the corresponding
               column.

       -l INT  Ignore reads shorter than INT

       -m, -d INT
               At a position, read at most INT reads per input file.  This means figures  greater
               than INT may be reported in the output.

               Setting this limit reduces the amount of memory and time needed to process regions
               with very high coverage.  Passing zero for this option  sets  it  to  the  highest
               possible value, effectively removing the depth limit. [8000]

               Note  that  up  to  release  1.8,  samtools would enforce a minimum value for this
               option.  This no longer happens and the limit is set exactly as specified.

       -o FILE Write output to FILE.  Using “-” for FILE will send the output to stdout (also the
               default if this option is not used).

       -q INT  Only count reads with base quality greater than INT

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

       -r CHR:FROM-TO
               Only report depth in specified region.

       -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  depth  [options]  -X  /data_folder/in1.bam  [/data_folder/in2.bam [...]]
               /index_folder/index1.bai [/index_folder/index2.bai [...]]

       -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]

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-mpileup(1), samtools-sort(1)

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