jvarkit

SamFindClippedRegions

Fins clipped position in one or more bam.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar samfindclippedregions  [options] Files

Usage: samfindclippedregions [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    --gtf
      Optional gtf file. Will be used to set a warning if the junction could 
      be a junction exon-exon of a retrogene. A GTF (General Transfer Format) 
      file. See https://www.ensembl.org/info/website/upload/gff.html . Please 
      note that CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --intron-distance
      when gtf is specified: max distance between breakend and the intron 
      bound 
      Default: 3
    --mapq
      min mapping quality
      Default: 1
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    --min-clip-depth
      Ignore if number of clipped bases overlaping one POS is lower than 'x'
      Default: 10
    --min-depth
      Ignore if Depth lower than 'x'
      Default: 10
    --min-ratio
      Ignore genotypes where count(clip)/(count(clip)+DP) < x
      Default: 0.1
    -o, --out
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --bed, --regions-file
      restrict to this bed file. A Bed file: (CHROM)<tab>(START 
      0-based)<tab>(END)[<tab>otherfields...]. 
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit
    -c
      consider only reads with clip having length >= 'x'
      Default: 1

Keywords

• sam
• bam
• clip
• vcf

Creation Date

20140228

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/SamFindClippedRegions.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/SamFindClippedRegionsTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite samfindclippedregions ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

samfindclippedregions find ‘blunt’ regions where the reads are clipped. It can be used to find structural variations in exomes/genomes data.

input is a set of indexed BAM/CRAM files or a list with the ‘.list’ suffix containing the path to the bam.

output is a VCF file

Example

$ java -jar dist/samfindclippedregions.jar --min-depth 10 --min-ratio 0.2 src/test/resources/S*.bam


##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=CL,Number=1,Type=Integer,Description="Left Clip">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=RL,Number=1,Type=Integer,Description="Right Clip">
##FORMAT=<ID=TL,Number=1,Type=Integer,Description="Total Clip">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
(...)
##samfindclippedregions.meta=compilation:20191009163450 githash:b8d60cab htsjdk:2.20.1 date:20191009163608 cmd:--min-depth 10 --min-ratio 0.2 src/test/resources/S1.bam src/test/resources/S2.bam src/test/resources/S3.bam src/test/resources/S4.bam src/test/resources/S5.bam
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4	S5
RF01	996	.	N	<CLIP>	.	.	AC=1;AF=0.1;AN=10;DP=30	GT:AD:CL:DP:RL:TL	0/0:2,0:0:2:0:0	0/0:4,0:0:4:0:00/0:4,0:0:4:0:0	0/0:15,0:0:15:0:0	0/1:4,1:0:5:1:1
(...)

Screenshot

https://twitter.com/yokofakun/status/1194921855875977216

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