samtools-depth(1)

1samtools-depth(1)            Bioinformatics tools            samtools-depth(1)
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NAME

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

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

14       Computes the depth at each position or region.
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OPTIONS

18       -a      Output all positions (including those with zero depth)
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20       -a -a, -aa
21               Output absolutely all positions, including unused reference se‐
22               quences.   Note  that  when used in conjunction with a BED file
23               the -a option may sometimes operate as if -aa was specified  if
24               the reference sequence has coverage outside of the region spec‐
25               ified in the BED file.
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27       -b FILE Compute depth at list of positions or regions in specified  BED
28               FILE.  []
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30       -f FILE Use  the  BAM files specified in the FILE (a file of filenames,
31               one file per line) []
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33       -H      Write a comment line showing column names at the  beginning  of
34               the  output.  The names are CHROM, POS, and then the input file
35               name for each depth column.  If one of  the  inputs  came  from
36               stdin, the name “-” will be used for the corresponding column.
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38       -l INT  Ignore  reads shorter than INT.  This is the number of bases in
39               the sequence, minus any soft clips.
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41       -m, -d INT
42               (Deprecated since 1.13)  This  option  previously  limited  the
43               depth  to  a maximum value.  It is still accepted as an option,
44               but ignored.
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46               Note for single files, the behaviour of old samtools  depth  -J
47               -q0  -d  INT FILE is identical to samtools mpileup -A -Q0 -x -d
48               INT FILE | cut -f 1,2,4
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50       -o FILE Write output to FILE.  Using “-” for FILE will send the  output
51               to stdout (also the default if this option is not used).
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53       -q, --min-BQ INT
54               Only count reads with base quality greater than or equal to INT
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56       -Q, --min-MQ INT
57               Only  count reads with mapping quality greater than or equal to
58               INT
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60       -r CHR:FROM-TO
61               Only report depth in specified region.
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63       -X      If this option is set, it will allow the user to  specify  cus‐
64               tomized index file location(s) if the data folder does not con‐
65               tain any index file. Example usage: samtools depth [options] -X
66               /data_folder/in1.bam    [/data_folder/in2.bam    [...]]    /in‐
67               dex_folder/index1.bai [/index_folder/index2.bai [...]]
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69       -g FLAGS
70               By default, reads that have any of the flags UNMAP,  SECONDARY,
71               QCFAIL,  or DUP set are skipped. To include these reads back in
72               the analysis, use this option together with the desired flag or
73               flag  combination.   FLAGS can be specified in hex by beginning
74               with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0'
75               (i.e.  /^0[0-7]+/),  as a decimal number not beginning with '0'
76               or as a comma-separated list of flag names. [0]
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78               For a list of flag names see samtools-flags(1).
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80       -G FLAGS
81               Discard any read that has any of the flags specified  by  FLAGS
82               set.   FLAGS  are  specified  as for the -g option. [UNMAP,SEC‐
83               ONDARY,QCFAIL,DUP]
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85       -J      Include reads with deletions in depth computation.
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87       -s      For the overlapping section of a  read  pair,  count  only  the
88               bases  of  the first read.  Note this algorithm changed in 1.13
89               so the results may differ slightly to older releases.
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CAVEATS

93       It may appear that "samtools depth" is simply "samtools  mpileup"  with
94       some  of  the columns removed, and indeed earlier versions of this com‐
95       mand were just this.  However both then and now there are  subtle  dif‐
96       ferences  in  parameters  which  make  the two not entirely comparable.
97       Differences, other than the obvious speed benefits, include:
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100       o Deletions (CIGAR element "D") are  ignored  by  default  in  "depth".
101         These  may  be  counted  by  adding  the -J option.  "Mpileup" always
102         counts the deleted bases, and has no option to toggle this.
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105       o Beware there are idiosyncrasies in option  naming.   Specifically  -q
106         and  -Q  options  have  their  meanings  swapped  between "depth" and
107         "mpileup".
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110       o The removal of overlapping sequences (option -s) is on by default  in
111         "mpileup"  and  off  by default in "depth".  Additionally the overlap
112         removal algorithm differs, giving subtle changes when Ns are  present
113         in  the sequence.  Also any paired read is considered for overlap re‐
114         moval by "depth", rather than only  those  with  the  properly-paired
115         flag set ("mpileup").  See above for a more detailed description.
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118       o The  default  minimum  quality  value  is  0  for  "depth" and 13 for
119         "mpileup".
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122       o Specifying multiple BAMs will produce one depth column per file  with
123         "depth", but these are merged in "mpileup".
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126       o "Depth"  doesn't have a maximum depth limit, while "mpileup" defaults
127         to a maximum of 8000.
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130       o If a reference is specified to "mpileup" the BAQ  algorithm  will  be
131         used  to adjust quality values, although it can be disabled.  "Depth"
132         never uses BAQ.
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AUTHOR

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

SYNOPSIS

DESCRIPTION

OPTIONS

CAVEATS

AUTHOR

SEE ALSO