RegenieFunctionalAnnot

Create annotation files for regenie using snpEff annotations

Usage

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

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

Usage: regeniefunctionalannot [options] Files
  Options:
  * -A, --annotations
      seq_ontology <-> score file. TSV file. no header. at least 2 columns 
      prediction_name/score 
    --gtf
      GTF file used to get first intron/intergenic.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --version
      print version and exit
    -f
      comma separated of Allele frequencies , This program will use the 
      highest freq to discard frequent variants.
      Default: 0.01
    -o
      Output file. Optional . Default: stdout

Keywords

• vcf
• regenie
• burden

Creation Date

20250311

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/regenie/RegenieFunctionalAnnot.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 regeniefunctionalannot ? 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

The aim of this class is to produce a file for regenie containing functional annotations with the following header:

"CONTIG","POS","ID","GENE","ANNOTATION","SCORE","CADD","FREQ","SINGLETON"

Example