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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]  [--tolerance]	 [--no-PG]  [-u]  -b  bed.file

       Clips  the  ends	 of read alignments if they intersect with regions de-
       fined in	a BED file.  While this	tool was originally written for	 clip-
       ping read alignment positions which correspond to amplicon primer loca-
       tions it	can also be used in other contexts.

       BED file	entries	used are chrom,	chromStart, chromEnd and,  optionally,
       strand.	 There	is a default tolerance of 5 bases when matching	chrom-
       Start and chromEnd to alignments.

       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 regions (e.g. amplicon primers) 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 the 5' and the 3' ends where regions match.

       --strand	  Use  strand  entry from the BED file to clip on the matching
		  forward or reverse alignment.

       --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.

       --tolerance INT
		  The  amount  of latitude given in matching regions to	align-
		  ments.  Default 5 bases.

       --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-1.13			  7 July 2021	      samtools-ampliconclip(1)


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