jvarkit

VcfGeneSplitter

Split VCF+VEP by gene/transcript.

Usage

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

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

Usage: vcfgenesplitter [options] Files
  Options:
    -e, -E, --extractors
      Gene Extractors Name. Space/semicolon/Comma separated. custom:tag is a 
      custom extractor extracting all the values for INFO/tag as one or more 
      gene name
      Default: ANN/GeneId VEP/GeneId
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ignore-filtered
      Ignore FILTERED variant
      Default: false
    -l, --list
      list all available extractors
    -m, --manifest
      Manifest Bed file output containing chrom/start/end of each gene
    -M, --max-variant
      Maximum number of variants required to write a vcf. don't write if 
      num(variant) > 'x' . '<=0' is ignore
      Default: -1
    -n, --min-variant
      Minimum number of variants required to write a vcf. don't write if 
      num(variant) < 'x'
      Default: 1
    --open-max
      Maximum number of opened VCF writers at the same time.
      Default: 100
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --version
      print version and exit

Keywords

• genes
• vcf

Creation Date

20160310

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfsplitgene/VcfGeneSplitter.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfsplitgene/VcfGeneSplitterTest.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 vcfgenesplitter ? 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/vcfgenesplitter.jar -o jeter.zip src/test/resources/rotavirus_rf.ann.vcf.gz -m jeter.mf

$ unzip -l jeter.zip
Archive:  jeter.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
     1565  2019-05-27 11:26   2c/8fb9d2539e3f30d1d9b06f9ec54c4c/Gene_18_3284.vcf.gz
     2278  2019-05-27 11:26   4e/4897c51fe2dd067a8b75c19f111477/Gene_1621_1636.vcf.gz
     2278  2019-05-27 11:26   74/ca4273c3d5803c5865891c808234da/UniProtKB_Swiss-Prot:P12472.vcf.gz
     2264  2019-05-27 11:26   23/6b59cfe4fdd33a5f4feeb55521dd34/Gene_50_2557.vcf.gz
     2169  2019-05-27 11:26   b3/4bda8d8502e64e442fce077e45ded6/Gene_9_2339.vcf.gz
     2106  2019-05-27 11:26   b7/83f96c410c7cd75bc732d44a1522a7/Gene_32_1507.vcf.gz
     2023  2019-05-27 11:26   6f/8472e9f192c92bf46e4893b2367b7e/Gene_23_1216.vcf.gz
     1862  2019-05-27 11:26   3c/513d82eaea18447dd5f621f92b40e6/Gene_0_1073.vcf.gz
     1655  2019-05-27 11:26   84/977eac8cdef861cbd3109209675d21/Gene_0_1058.vcf.gz
     1754  2019-05-27 11:26   db/aee9cc8f5c9c3d39c7af4cec63b7a5/Gene_0_1061.vcf.gz
     1746  2019-05-27 11:26   b0/133c483f0ea676f8d29ab1f2daee5d/Gene_41_568.vcf.gz
     1664  2019-05-27 11:26   59/0fd5c1e8d6d60a986a0021fe357514/Gene_20_616.vcf.gz
     1663  2019-05-27 11:26   83/bc905cf311428ab80ce59aaf503838/Gene_78_374.vcf.gz
---------                     -------
    25027                     13 files

$ cat jeter.mf
#chrom	start	end	key	path	Count_Variants
RF01	969	970	ANN/GeneId	Gene_18_3284	2c/8fb9d2539e3f30d1d9b06f9ec54c4c/Gene_18_3284.vcf.gz	1
RF02	250	1965	ANN/GeneId	Gene_1621_1636	4e/4897c51fe2dd067a8b75c19f111477/Gene_1621_1636.vcf.gz	5
RF02	250	1965	ANN/GeneId	UniProtKB/Swiss-Prot:P12472	74/ca4273c3d5803c5865891c808234da/UniProtKB_Swiss-Prot:P12472.vcf.gz	5
RF03	1220	2573	ANN/GeneId	Gene_50_2557	23/6b59cfe4fdd33a5f4feeb55521dd34/Gene_50_2557.vcf.gz	8
RF04	886	1920	ANN/GeneId	Gene_9_2339	b3/4bda8d8502e64e442fce077e45ded6/Gene_9_2339.vcf.gz	7
RF05	40	1339	ANN/GeneId	Gene_32_1507	b7/83f96c410c7cd75bc732d44a1522a7/Gene_32_1507.vcf.gz	6
RF06	516	1132	ANN/GeneId	Gene_23_1216	6f/8472e9f192c92bf46e4893b2367b7e/Gene_23_1216.vcf.gz	5
RF07	97	952	ANN/GeneId	Gene_0_1073	3c/513d82eaea18447dd5f621f92b40e6/Gene_0_1073.vcf.gz	4
RF08	925	992	ANN/GeneId	Gene_0_1058	84/977eac8cdef861cbd3109209675d21/Gene_0_1058.vcf.gz	2
RF09	293	414	ANN/GeneId	Gene_0_1061	db/aee9cc8f5c9c3d39c7af4cec63b7a5/Gene_0_1061.vcf.gz	3
RF10	45	175	ANN/GeneId	Gene_41_568	b0/133c483f0ea676f8d29ab1f2daee5d/Gene_41_568.vcf.gz	3
RF11	73	79	ANN/GeneId	Gene_20_616	59/0fd5c1e8d6d60a986a0021fe357514/Gene_20_616.vcf.gz	1
RF11	73	79	ANN/GeneId	Gene_78_374	83/bc905cf311428ab80ce59aaf503838/Gene_78_374.vcf.gz	1

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