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/>