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samtools-ampliconclip(1)     Bioinformatics tools     samtools-ampliconclip(1)

       samtools	ampliconclip - clip reads using	a BED file

       samtools	  ampliconclip	[-o  out.file]	[-f  stat.file]	 [--soft-clip]
       [--hard-clip] [--both-ends] [--strand] [--clipped] [--fail]  [--filter-
       len INT]	[--fail-len INT] [--no-excluded] [--rejects-file rejects.file]
       [--original] [--keep-tag] [--no-PG] [-u]	-b bed.file in.file

       Clip reads in a SAM compatible file based on data from a	BED file.   By
       default	the  reads  are	soft clipped and clip is only done from	the 5'

       Some things to be aware of.  While ordering is not significant, adjust-
       ments to	the left most mapping position (POS) will mean that coordinate
       sorted files will need resorting.  In such cases	the sorting  order  in
       the  header  is	set  to	unknown. Clipping of reads results in template
       length (TLEN) being incorrect. This can be corrected by	samtools  fix-
       mates.	Any  MD	 and  NM aux tags will also be incorrect, which	can be
       fixed by	samtools calmd.	 By default MD and NM tags are removed	though
       if the output is	in CRAM	format these tags will be automatically	regen-

       -b FILE	  BED file of amplicons	to be removed.

       -o FILE	  Output file name (defaults to	stdout).

       -f FILE	  File to write	stats to (defaults to stderr).

       -u	  Output uncompressed SAM, BAM or CRAM.

		  Soft clip reads (default).

		  Hard clip reads.

		  Clip at both ends as opposed to just the 5' end.

       --strand	  Use strand entry from	the BED	file.

       --clipped  Only output clipped reads.  Filter all others.

       --fail	  Mark unclipped reads as QC fail.

       --filter-len INT
		  Filter out reads of INT size or shorter.  In this case  soft
		  clips	 are not counted toward	read length.  An INT of	0 will
		  filter out reads with	no matching bases.

       --fail-len INT
		  As --filter-len but mark as QC fail rather then filter out.

		  Filter out any reads that are	marked as QCFAIL  or  are  un-
		  mapped.   This  works	on the state of	the reads before clip-
		  ping takes place.

       --rejects-file FILE
		  Write	any filtered reads out to a file.

       --original Add an OA tag	with the original data for clipped files.

       --keep-tag In clipped reads, keep the possibly invalid NM and MD	 tags.
		  By default these tags	are deleted.

       --no-PG	  Do not at a PG line to the header.

       Written	by Andrew Whitwham and Rob Davies, both	from the Sanger	Insti-

       samtools(1), samtools-sort(1), samtools-fixmate(1), samtools-calmd(1)

       Samtools	website: <>

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


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