samtools-depth - computes the read depth at each position or region
samtools depth [
options] [
in1.sam|
in1.bam|
in1.cram
[
in2.sam|
in2.bam|
in2.cram] [...]]
Computes the depth at each position or region.
- -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
- 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]
- -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.
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.
Written by Heng Li and James Bonfield from the Sanger Institute.
samtools(1),
samtools-mpileup(1),
samtools-coverage(1),
samtools-sort(1)
Samtools website: <
http://www.htslib.org/>