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

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 se-
	       quences.	  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 spec-
	       ified 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 or equal	to INT

       -Q 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	allows user to specify custom-
	       ized 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	[...]]	  /in-
	       dex_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,SEC-
	       ONDARY,QCFAIL,DUP]

       -J      Include reads with deletions in depth computation.

       -s      For  the	 overlapping  section  of  a read pair,	count only the
	       bases of	a single read. This is accomplished by lowering	 to  0
	       the  quality values of one read for the span of the overlapping
	       section.	As a consequence, the  algorithm  will	consider  only
	       bases with a quality above 0.

AUTHOR
       Written by Heng Li from the Sanger Institute.

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

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

samtools-1.11		       22 September 2020	     samtools-depth(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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