jvarkit

VCFBedSetFilter

Set FILTER for VCF if intersects with BED.

Usage

Usage: java -jar dist/vcfbedsetfilter.jar  [options] Files
Usage: vcfbedsetfilter [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
    -e, --exclude, --blacklist
      Tribble or Tabix bed file containing the regions to be FILTERED. Must be 
      indexed with tribble or tabix, or use '--fast' to load in memory.
    -x, --extend
      Extend the variant coordinates per 'x' bases. A distance specified as a 
      positive integer.Commas are removed. The following suffixes are 
      interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 0
    -f, --filter
      FILTER name. If `--filter` is empty, FILTERED variant will be discarded.
      Default: VCFBED
    --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].
    --fast, --memory
      Load the bed in memory: faster than tribble/tabix but memory consumming)
      Default: false
    --min-bed-fraction
      Min BED fraction overlap after extension. Only consider BED records if 
      variant overlap >= 'x' percent of bed length. A decimal number between 
      0.0 and 1.0. If the value ends with '%' it is interpretted as a 
      percentage eg. '1%' => '0.01'. A slash '/' is interpretted as a ratio. 
      e.g: '1/100' => '0.01'.
    --min-vc-fraction
      Min Variant fraction overlap after extension. Only consider BED records 
      if bed overlap >= 'x' percent of vc length. A decimal number between 0.0 
      and 1.0. If the value ends with '%' it is interpretted as a percentage 
      eg. '1%' => '0.01'. A slash '/' is interpretted as a ratio. e.g: '1/100' 
      => '0.01'.
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -i, --include, --whitelist
      Tribble or Tabix bed file containing the regions to be accepted. Regions 
      NOT overlapping those regions will be FILTERED. Must be indexed with 
      tribble or tabix, or use '--fast' to load in memory.

Keywords

• vcf
• bed
• filter

See also in Biostars

• https://www.biostars.org/p/9465226

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

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

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

Creation Date

20150415

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfbed/VCFBedSetFilter.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfbed/VCFBedSetFilterTest.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 vcfbedsetfilter ? 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

Examples

$java -jar dist/vcfbedsetfilter.jar -f MYFILTER - -B in.bed in.vcf 

history:

2191104: changed the logic which was wrongly defined in the documentation. :-/

Cited in

• Megquier K, Turner-Maier J, Morrill K, Li X, Johnson J, Karlsson EK, et al. (2022) The genomic landscape of canine osteosarcoma cell lines reveals conserved structural complexity and pathway alterations. PLoS ONE 17(9): e0274383. https://doi.org/10.1371/journal.pone.0274383

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