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samtools-ampliconclip(1) Bioinformatics tools samtools-ampliconclip(1) NAME samtools ampliconclip - clip reads using a BED file SYNOPSIS samtools ampliconclip [-o out.file] [-f stat.file] [--soft-clip] [--hard- clip] [--both-ends] [--strand] [--clipped] [--fail] [--filter-len INT] [--fail-len INT] [--unmap-len INT] [--no-excluded] [--rejects-file re- jects.file] [--original] [--keep-tag] [--tolerance] [--no-PG] [-u] -b bed.file in.file DESCRIPTION Clips the ends of read alignments if they intersect with regions defined in a BED file. While this tool was originally written for clipping read alignment positions which correspond to amplicon primer locations it can also be used in other contexts. BED file entries used are chrom, chromStart, chromEnd and, optionally, strand. Standard BED file format must be used, so if strand is needed then the name and score fields must also be present (even though ampliconclip does not read them). There is a default tolerance of 5 bases when matching chromStart and chromEnd to alignments. By default the reads are soft clipped and clip is only done from the 5' end. Some things to be aware of. While ordering is not significant, adjustments 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) be- ing incorrect. This can be corrected by samtools fixmates. 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 regenerated. OPTIONS -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 Soft clip reads (default). --hard-clip Hard clip reads. --both-ends Clip at both the 5' and the 3' ends where regions match. When using this option the --strand option is ignored. --strand Use strand entry from the BED file to clip on the matching for- ward 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 fil- ter out reads with no matching bases. --fail-len INT As --filter-len but mark as QC fail rather then filter out. --unmap-len INT As --filter-len but mark as unmapped. Default is 0 (no matching reads). -1 will disable. --no-excluded Filter out any reads that are marked as QCFAIL or are unmapped. This works on the state of the reads before clipping takes place. --rejects-file FILE Write any filtered reads out to a file. --primer-counts FILE File to write with read counts per bed entry (bedgraph format). --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 alignments. Default 5 bases. --no-PG Do not at a PG line to the header. AUTHOR Written by Andrew Whitwham and Rob Davies, both from the Sanger Institute. SEE ALSO samtools(1), samtools-sort(1), samtools-fixmate(1), samtools-calmd(1) Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-ampliconclip(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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