jvarkit

GtfRetroCopy

Scan retrocopies by comparing the gtf/intron and the deletions in a VCF

Usage

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

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

Usage: gtfretrocopy [options] Files
  Options:
    --all
      all introns must be found
      Default: false
    --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
  * -gtf, --gtf
      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].
    --id, -id
      Which key should I use for the column ID. The idea is to use the gene 
      name to get the uniq entities per vcf.
      Default: transcript_id
      Possible Values: [transcript_id, gene_id, gene_name]
    -k, --known
      Gene-ID of known retrogenes. One per line. A source could be : 
      http://retrogenedb.amu.edu.pl/static/download/ 
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• gtf
• retrocopy
• deletion

Creation Date

20190813

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/retrocopy/GtfRetroCopyTest.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 gtfretrocopy ? 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/gtfretrocopy.jar --gtf transcript.gtf.gz input.vcf.gz > retrocopies.vcf

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