jvarkit

VcfGnomadSV

Peek annotations from gnomad structural variants

Usage

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

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

Usage: vcfgnomadsv [options] Files
  Options:
    --any-overlap-filter
      If not empty, set this FILTER if any variant in gnomad is found 
      overlaping the variant BUT we didn't find a correct match
      Default: <empty string>
    --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
    --bnd-distance
      Two BND variants are the same if their bounds are distant by less than 
      xxx 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: 100
    --check-bnd-mate
      When comparing two BND, check that their mate (using the ALT allele) are 
      the same too
      Default: false
    --discordant_svtype
      If not empty, set this FILTER if SVTYPE are discordants
      Default: <empty string>
    --filter
      set this FILTER is the allele frequency found in the population is not 
      min-af<=x<=max-af. Discard variant if it is blank.
      Default: BAD_AF
    --force-svtype
      When comparing two SV variants, their INFO/SVTYPE should be the same. 
      Default is to just use coordinates to compare non-BND variants.
      Default: false
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
  * -g, --gnomad
      Gnomad-SV VCF file. see 
      https://gnomad.broadinstitute.org/downloads#structural-variants 
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --in-gnomad-filter
      If not empty, set this FILTER is variant was found in gnomad
      Default: <empty string>
    --max-af
      max allele frequency in watched population. 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'.
      Default: 1.0
    --min-af
      min allele frequency in watched population. 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'.
      Default: 0.0
    -o, --out
      Output file. Optional . Default: stdout
    --population
      Watch gnomad population for AF
      Default: POPMAX_AF
    -p, --prefix
      INFO field prefix
      Default: GNOMAD_
    --sv-alleles-bases
      When comparing two non-BND SV variants, use their ALT alleles to adjust 
      the interval. It solves the problem of  
      'chr2:10556028:AATTATATAATTAAATTAATTATATAATT:A'  vs 
      'chr2:10556028:A:AATTATATAATTAAATTAATTATATAATT'. See 
      https://twitter.com/yokofakun/status/1169182491606999046 
      Default: false
    --sv-overlap-fraction
      Two CNV/DEL/.. variants are the same if they share 'x' fraction of their 
      size. 
      Default: 0.75
    --sv-small-overlap
      Two non-BND variants are the same if they overlap and both have a 
      length<= 'x'. A distance specified as a positive integer.Commas are 
      removed. The following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 10
    --version
      print version and exit

Keywords

• vcf
• annotation
• gnomad
• sv

Creation Date

20190814

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gnomad/VcfGnomadSV.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/gnomad/VcfGnomadSVTest.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 vcfgnomadsv ? 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/vcfgnomadsv.jar \
	-g src/test/resources/gnomad_v2_sv.sites.vcf.gz \
	./src/test/resources/manta.B00GWGD.vcf.gz

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