jvarkit

StarRetroCopy

Scan retrocopies from the star-aligner/bwa output

Usage

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

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

Usage: starretrocopy [options] Files
  Options:
    --bedpe, -P, -J
      Optional. Save possible sites of insertion in this Bed-PE file.
  * -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].
    --mapq, -mapq
      Min mapping quality
      Default: 1
    -n, --min-cigar-size
      Minimal cigar element length for clipped sequence.
      Default: 6
    --min-depth, -D
      In a transcript one must found at least 'D' reads with a clip-length> 
      'min-cigar-size'. 
      Default: 1
    --no-ji, --no-star, --bwa
      Do not use the 'Ji' Attribute generated by STAR aligner to get the 
      intron bounds but use the CIGAR string (e.g: output of bwa)
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -r, -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict Can 
      be used for reading CRAM.
    --bam, --save-bam
      Optional: save matching reads in this bam file. Can be used to visualize 
      the evidences in IGV.
    --transcript-id
      Limit to those transcript ID (one id per line)
    --version
      print version and exit
    --bai, -bai, --with-bai
      Use random access BAM using the bai and using the GTF data. May be slow 
      at startup
      Default: false

Keywords

• sam
• bam
• cigar
• clip
• sv
• retrocopy
• star

Creation Date

20190710

Source code

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

Unit Tests

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

This site is open source. Improve this page.