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.   This  is the number of bases in the sequence, minus any soft
               clips.

       -m, -d INT
               (Deprecated since 1.13) This option previously limited the depth to a maximum value.  It is still
               accepted as an option, but ignored.

               Note for single files, the behaviour of old samtools depth -J -q0 -d INT  FILE  is  identical  to
               samtools mpileup -A -Q0 -x -d INT FILE | cut -f 1,2,4

       -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, --min-BQ INT
               Only count reads with base quality greater than or equal to INT

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

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

       -X      If this option is set, it will allow the 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, --excl-flags FLAGS
               Discard reads that have any of the flags specified by FLAGS set.  FLAGS are specified as for  the
               -g option. [UNMAP,SECONDARY,QCFAIL,DUP]

       --incl-flags FLAGS
               Only  include  reads  with  at  least  one bit set in FLAGS present in the FLAG field.  FLAGS are
               specified as for the -g option. [0]

       --require-flags FLAGS
               Only include reads with all bits set in FLAGS present in the FLAG field.  FLAGS are specified  as
               for the -g option. [0]

       -J      Include reads with deletions in depth computation.

       -s      For  the  overlapping  section of a read pair, count only the bases of the first read.  Note this
               algorithm changed in 1.13 so the results may differ slightly to older releases.

CAVEATS

       It may appear that "samtools depth" is simply "samtools mpileup" with some of the  columns  removed,  and
       indeed  earlier  versions  of  this  command  were just this.  However both then and now there are subtle
       differences in parameters which make the two  not  entirely  comparable.   Differences,  other  than  the
       obvious speed benefits, include:

       o Deletions (CIGAR element "D") are ignored by default in "depth".  These may be counted by adding the -J
         option.  "Mpileup" always counts the deleted bases, and has no option to toggle this.

       o Beware  there  are idiosyncrasies in option naming.  Specifically -q and -Q options have their meanings
         swapped between "depth" and "mpileup".

       o The removal of overlapping sequences (option -s) is on by default in "mpileup" and off  by  default  in
         "depth".  Additionally the overlap removal algorithm differs, giving subtle changes when Ns are present
         in  the  sequence.  Also any paired read is considered for overlap removal by "depth", rather than only
         those with the properly-paired flag set ("mpileup").  See above for a more detailed description.

       o The default minimum quality value is 0 for "depth" and 13 for "mpileup".

       o Specifying multiple BAMs will produce one depth column per file with "depth", but these are  merged  in
         "mpileup".

       o "Depth" doesn't have a maximum depth limit, while "mpileup" defaults to a maximum of 8000.

       o If  a  reference  is  specified  to  "mpileup" the BAQ algorithm will be used to adjust quality values,
         although it can be disabled.  "Depth" never uses BAQ.

AUTHOR

       Written by Heng Li and James Bonfield from the Sanger Institute.

SEE ALSO

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

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

samtools-1.19.2                                  24 January 2024                               samtools-depth(1)