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 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/>