jvarkit

Biostar332826

Last commit

Fast Extraction of Variants from a list of IDs

Usage

Usage: biostar332826 [options] Files
  Options:
    -d, --delete
      When found , remove the ID from the list of identifiers. Should be 
      faster but don't use it if two variants have the same ID.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -r, -i, --ids
      A list of identifiers, one per line
    -v, --inverse
      Inverse: don't print the variants containing the IDS.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -R, -I
      A semicolon/comma/space separated list of identifiers
      Default: <empty string>

Keywords

See also in Biostars

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar332826

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar332826.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar332826Test.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite biostar332826 ? 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

 $ wget -O - -q "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" |\
 	gunzip -c |\
 	java -jar dist/biostar332826 --ids ids.txt > out.vcf