RegenieBedAnnot

Last commit

Create annotation files for regenie using BED annotations

Usage

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

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

Usage: regeniebedannot [options] Files
  Options:
  * -B, --bed
      custom bed file chrom/start/end/annotation/name[/score].
    --chrom
      process only that chromosome
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --min-length
      slop each BED records in 5' and 3' so the minimal LENGTH is 'm'. 
      Multiple are comma separated
      Default: 0
    --noXY
      skip X/Y chromosome
      Default: false
    --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/RegenieBedAnnot.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 regeniebedannot ? 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 from a bed file

CHROM START END ANNOTATION TITLE

and to generate a file

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

that can be piped into RegeniemakeAnnot