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 rejects.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)  being
       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 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.

       --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-1.21                                   12 September 2024                       samtools-ampliconclip(1)