jvarkit

VcfAfInfoFilter

Filter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomad

Usage

Usage: vcfafinfofilter [options] Files
  Options:
    -A, --any
      [20190723] Set the FILTER if **ANY** alt allele is over the threshold
      Default: false
    --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
    --disable-vc-attribute-recalc
      When genotypes are removed/changed, Dd not recalculate variant 
      attributes like DP, AF, AC, AN...
      Default: false
    -F, --fields
      [20180905]How to extract the AlleleFrequencies from a variant. Multiple 
      separated with comma or semicolon. e.g: 
      "AC/AN;exome_CEU_*;genome_NFE_AF;another_AC/another/AN". Input is a set 
      of AC/AN field pairs or/and AF field separated by semicolon. 'x/y' means 
      AC/AN fields. '*' will be replaced with AC and AN, hence, 'exome_CEU_*' 
      will be interpreted as exome_CEU_AC/exome_CEU_AN. Other field will be 
      interpreted as an AF field.
      Default: <empty string>
    --filter, -f
      set this filter if all ALT fails the treshold. If empty :remove the 
      variant 
      Default: <empty string>
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    --gtfilter, -gtf
      set this *GENOTYPE* filter if all ALT for a Genotype fail the treshold. 
      If empty :set genotype to NO_CALL
      Default: HIGH_AF
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --min-af
      Min for allele Frequency. ALT alleles under this AF value will be 
      subject to filtration. 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
    -nfe, --nfe
      Add INFO fields for the 'NFE' population created by vcfgnomad: gnomad_exome_AC_NFE,gnomad_exome_AF_NFE,gnomad_exome_AN_NFE,gnomad_genome_AC_NFE,gnomad_genome_AF_NFE,gnomad_genome_AN_NF
      Default: false
    -i, --no-valid
      Ignore INFO Field Validation. (e.g INFO field not declarated in VCF 
      header) 
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --treshold, -t, --max-af
      Treshold for allele Frequency. Maximum. ALT alleles above this AF value 
      will be subject to filtration. 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: 0.001
    --vc-attribute-recalc-ignore-filtered
      When recalculating variant attributes like DP AF, AC, AN, ignore 
      FILTERed **Genotypes**
      Default: false
    --vc-attribute-recalc-ignore-missing
      Ignore missing VCF headers (DP, AF, AC, AN). Default behavior: adding 
      VCF header if they're missing
      Default: false
    --version
      print version and exit

Keywords

• vcf
• annotation
• af

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 vcfafinfofilter

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

Creation Date

20180625

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfAfInfoFilter.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/VcfAfInfoFilterTest.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 vcfafinfofilter ? 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

Motivation

I’m often asked to filter out variant that are too frequent in gnomad, but I must keep the data if any ALT allele is NOT in gnomad.

This tool filters VCF containing external allele frequency information (AF or AC/AN). Used as a complement of VcfGnomadPext.

Example

$ java -jar dist/vcfafinfofilter.jar -nfe input.vcf
$ java -jar dist/vcfafinfofilter.jar -af 'gnomad_exome_AF_NFE,gnomad_genome_AF_NFE'   input.vcf
$ java -jar dist/vcfafinfofilter.jar -acn 'gnomad_genome_AC_NFE,gnomad_genome_AN_NFE'   input.vcf
$ java -jar dist/vcfafinfofilter.jar -acn 'gnomad_genome_*_NFE'   input.vcf

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