TranslateGff3

Last commit

translates the output of bcftools consensus

Usage

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

Usage: java -jar dist/jvarkit.jar translategff3  [options] Files

Usage: translategff3 [options] Files
  Options:
  * --gff, --gff3
      Gff3 file
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

gff
gff3
fasta
genpred
peptide
protein

Creation Date

20241003

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/translategff3/TranslateGff3.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 translategff3 ? 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

Experimental. Translates the output of bcftools consensus. Output is a BED file containing the cDNA, the translated peptide and the mean codon usage .

Example

samtools faidx ref.fa 8:11870-11890 |\
    bcftools consensus in.vcf.gz  -s SAMPLE -H A --include 'TYPE="snp"' |\
    java -jar dist/jvarkit.jar translategff3 --gff3 annot.gff3