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:
    -e, -E, --extractors
      Gene Extractors Name. Space/semicolon/Comma separated
      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