1samtools-ampliconclip(1)     Bioinformatics tools     samtools-ampliconclip(1)
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NAME

6       samtools ampliconclip - clip reads using a BED file
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SYNOPSIS

9       samtools   ampliconclip  [-o  out.file]  [-f  stat.file]  [--soft-clip]
10       [--hard-clip] [--both-ends] [--strand] [--clipped] [--fail]  [--filter-
11       len INT] [--fail-len INT] [--no-excluded] [--rejects-file rejects.file]
12       [--original] [--keep-tag]  [--tolerance]  [--no-PG]  [-u]  -b  bed.file
13       in.file
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DESCRIPTION

17       Clips  the  ends  of read alignments if they intersect with regions de‐
18       fined in a BED file.  While this tool was originally written for  clip‐
19       ping read alignment positions which correspond to amplicon primer loca‐
20       tions it can also be used in other contexts.
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22       BED file entries used are chrom, chromStart, chromEnd and,  optionally,
23       strand.   There  is a default tolerance of 5 bases when matching chrom‐
24       Start and chromEnd to alignments.
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26       By default the reads are soft clipped and clip is only done from the 5'
27       end.
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29       Some things to be aware of.  While ordering is not significant, adjust‐
30       ments to the left most mapping position (POS) will mean that coordinate
31       sorted  files  will need resorting.  In such cases the sorting order in
32       the header is set to unknown. Clipping of  reads  results  in  template
33       length  (TLEN)  being incorrect. This can be corrected by samtools fix‐
34       mates.  Any MD and NM aux tags will also be  incorrect,  which  can  be
35       fixed  by samtools calmd.  By default MD and NM tags are removed though
36       if the output is in CRAM format these tags will be automatically regen‐
37       erated.
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OPTIONS

41       -b FILE    BED file of regions (e.g. amplicon primers) to be removed.
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43       -o FILE    Output file name (defaults to stdout).
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45       -f FILE    File to write stats to (defaults to stderr).
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47       -u         Output uncompressed SAM, BAM or CRAM.
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49       --soft-clip
50                  Soft clip reads (default).
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52       --hard-clip
53                  Hard clip reads.
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55       --both-ends
56                  Clip at both the 5' and the 3' ends where regions match.
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58       --strand   Use  strand  entry from the BED file to clip on the matching
59                  forward or reverse alignment.
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61       --clipped  Only output clipped reads.  Filter all others.
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63       --fail     Mark unclipped reads as QC fail.
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65       --filter-len INT
66                  Filter out reads of INT size or shorter.  In this case  soft
67                  clips  are not counted toward read length.  An INT of 0 will
68                  filter out reads with no matching bases.
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70       --fail-len INT
71                  As --filter-len but mark as QC fail rather then filter out.
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73       --no-excluded
74                  Filter out any reads that are marked as QCFAIL  or  are  un‐
75                  mapped.   This  works on the state of the reads before clip‐
76                  ping takes place.
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78       --rejects-file FILE
79                  Write any filtered reads out to a file.
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81       --original Add an OA tag with the original data for clipped files.
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83       --keep-tag In clipped reads, keep the possibly invalid NM and MD  tags.
84                  By default these tags are deleted.
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86       --tolerance INT
87                  The  amount  of latitude given in matching regions to align‐
88                  ments.  Default 5 bases.
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90       --no-PG    Do not at a PG line to the header.
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AUTHOR

94       Written by Andrew Whitwham and Rob Davies, both from the Sanger  Insti‐
95       tute.
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SEE ALSO

99       samtools(1), samtools-sort(1), samtools-fixmate(1), samtools-calmd(1)
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101       Samtools website: <http://www.htslib.org/>
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105samtools-1.13                     7 July 2021         samtools-ampliconclip(1)
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