jvarkit

VcfGeneSplitter

Last commit

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:
    --disable-hash-directory, --dhd
      disable default which is to save each file in a checksum-based 
      directory-a-la-nextflow to avoid a large number of files in the same 
      directory. 
      Default: false
    -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. +x is a custom extractor using sliding windows of integer 
      size=x (e.g: '+10000' or '+1Mb' )
      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/POS of each gene
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --prefix
      prefix each output VCF file with this string
      Default: <empty string>
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --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	POS	key	path	Count_Variants
RF01	969		ANN/GeneId	Gene_18_3284	2c/8fb9d2539e3f30d1d9b06f9ec54c4c/Gene_18_3284.vcf.gz	1
RF02	250		ANN/GeneId	Gene_1621_1636	4e/4897c51fe2dd067a8b75c19f111477/Gene_1621_1636.vcf.gz	5
RF02	250		ANN/GeneId	UniProtKB/Swiss-Prot:P12472	74/ca4273c3d5803c5865891c808234da/UniProtKB_Swiss-Prot:P12472.vcf.gz	5
RF03	1220		ANN/GeneId	Gene_50_2557	23/6b59cfe4fdd33a5f4feeb55521dd34/Gene_50_2557.vcf.gz	8
RF04	886		ANN/GeneId	Gene_9_2339	b3/4bda8d8502e64e442fce077e45ded6/Gene_9_2339.vcf.gz	7
RF05	40		ANN/GeneId	Gene_32_1507	b7/83f96c410c7cd75bc732d44a1522a7/Gene_32_1507.vcf.gz	6
RF06	516		ANN/GeneId	Gene_23_1216	6f/8472e9f192c92bf46e4893b2367b7e/Gene_23_1216.vcf.gz	5
RF07	97		ANN/GeneId	Gene_0_1073	3c/513d82eaea18447dd5f621f92b40e6/Gene_0_1073.vcf.gz	4
RF08	925		ANN/GeneId	Gene_0_1058	84/977eac8cdef861cbd3109209675d21/Gene_0_1058.vcf.gz	2
RF09	293		ANN/GeneId	Gene_0_1061	db/aee9cc8f5c9c3d39c7af4cec63b7a5/Gene_0_1061.vcf.gz	3
RF10	45		ANN/GeneId	Gene_41_568	b0/133c483f0ea676f8d29ab1f2daee5d/Gene_41_568.vcf.gz	3
RF11	73		ANN/GeneId	Gene_20_616	59/0fd5c1e8d6d60a986a0021fe357514/Gene_20_616.vcf.gz	1
RF11	73		ANN/GeneId	Gene_78_374	83/bc905cf311428ab80ce59aaf503838/Gene_78_374.vcf.gz	1