jvarkit

KnownRetroCopy

Annotate VCF structural variants that could be intron from retrocopies.

Usage

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

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

Usage: knownretrocopy [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
    -d, --distance
      max distance between an intron and the deletion found in the VCF
      Default: 10
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -k, --known
      Gene-ID of known retrogenes. One per line. A source could be : 
      http://retrogenedb.amu.edu.pl/static/download/ 
    -o, --out
      Output file. Optional . Default: stdout
  * -genpred, --genpred, --kg, --transcripts
      Transcrips as genpred format 
      https://genome.ucsc.edu/FAQ/FAQformat.html#format9  . The genePred 
      format is a compact alternative to GFF/GTF because one transcript is 
      described using only one line.	Beware chromosome names are formatted the 
      same as your REFERENCE. A typical KnownGene file is 
      http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz 
      .If you only have a gff file, you can try to generate a knownGene file 
      with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
    --version
      print version and exit

Keywords

• gtf
• retrocopy
• deletion

Creation Date

20190815

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/retrocopy/KnownRetroCopy.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/retrocopy/KnownRetroCopyTest.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 knownretrocopy ? 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

Example

$ java -jar dist/knownretrocopy.jar --gtf Homo_sapiens.GRCh37.87.gtf.gz candidateSV.vcf.gz | grep RETR

##FILTER=<ID=RETROCOPY_INTRON,Description="variant could be a deleted intron from a retrocopy">
##FILTER=<ID=RETROCOPY_KNOWN,Description="variant could be a deleted intron from a known retrocopy">
##INFO=<ID=RETROCOPY,Number=.,Type=String,Description="Identifiers for the retrocopies.">
chr1	38077349	MantaDEL:2204:0:0:0:0:0	CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA	C	.RETROCOPY_INTRON	CIGAR=1M71D;DOWNSTREAM_PAIR_COUNT=0;END=38077420;PAIR_COUNT=0;RETROCOPY=ENSG00000169218,ENST00000356545,ENST00000401071,RSPO1,RSPO1-201,RSPO1-202;SVLEN=-71;SVTYPE=DEL;UPSTREAM_PAIR_COUNT=0
chr1	38077349	MantaDEL:2204:0:1:0:0:0	CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA	C	.RETROCOPY_INTRON	CIGAR=1M71D;DOWNSTREAM_PAIR_COUNT=0;END=38077420;PAIR_COUNT=0;RETROCOPY=ENSG00000169218,ENST00000356545,ENST00000401071,RSPO1,RSPO1-201,RSPO1-202;SVLEN=-71;SVTYPE=DEL;UPSTREAM_PAIR_COUNT=0
chr1	38077349	MantaDEL:2204:1:1:0:0:0	CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA	C	.RETROCOPY_INTRON	CIGAR=1M71D;DOWNSTREAM_PAIR_COUNT=0;END=38077420;PAIR_COUNT=0;RETROCOPY=ENSG00000169218,ENST00000356545,ENST00000401071,RSPO1,RSPO1-201,RSPO1-202;SVLEN=-71;SVTYPE=DEL;UPSTREAM_PAIR_COUNT=0
(...)

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