jvarkit

VCFPolyX

Last commit

Number of repeated REF bases around POS.

Usage

Usage: vcfpolyx [options] Files
  Options:
    --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
    -n, --filter
      if number of repeated bases is greater or equal to 'n' set a FILTER = 
      (tag) 
      Default: -1
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --skip-filtered
      Don't spend some time to calculate the tag if the variant is FILTERed
      Default: false
    -t, --tag
      Tag used in INFO and FILTER columns.
      Default: POLYX
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfpolyx

The java jar file will be installed in the dist directory.

Creation Date

20200930

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfpolyx/VCFPolyX.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfpolyx/VCFPolyXTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfpolyx ? 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/vcfpolyx.jar -R reference.fa input.vcf
(...)
2   1133956 .   A   G   2468.84 .   POLYX=23
2   1133956 .   A   AG  3604.25 .   POLYX=23
2   2981671 .   T   G   47.18   .   POLYX=24
(...)

Cited in: