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.

       --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/>