jvarkit

Biostar332826

Fast Extraction of Variants from a list of IDs

Usage

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

Usage: java -jar dist/jvarkit.jar biostar332826  [options] Files

Usage: biostar332826 [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
    -d, --delete
      When found , remove the ID from the list of identifiers unless it's a 
      '.'. Should be faster but don't use it if two variants have the same ID.
      Default: false
    -f, --filter
      if not blank soft filter the variants that are NOT in the list. If 
      '--inverse' is specified then soft-filter the variants IN the list.
    --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].
    -r, -i, --ids
      A list of identifiers, one per line
    --inverse
      Inverse: don't print the variants containing the IDS.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -R, -I
      A semicolon/comma/space separated list of identifiers
      Default: <empty string>

Keywords

• vcf
• rs
• id

See also in Biostars

• https://www.biostars.org/p/332826
• https://www.biostars.org/p/433062

Creation Date

20180817

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

• 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 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 

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