jvarkit

VcfBurdenFisherH

Last commit

Fisher Case /Controls per Variant

Usage

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

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

Usage: vcfburdenfisherh [options] Files
  Options:
    --attribute
      Name of the attribute used for INFO
      Default: BurdenHFisher
    --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
    -F2, --ctrlgtcase
      Set this FILTER if the proportion of Controls carrying a ALT allele is 
      creater than proportion of CASES. if blank, variant is discarded.
      Default: CTRL_CASE_RATIO
    -F1, --filter
      if this value is not blank, the FILTER will be set for this variant if 
      the fisher values are out of the bounds.
      Default: BurdenHFisher
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -gtf, --gtf, --gtFiltered
      [20180115] Ignore FILTERed **Genotype**
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -ignoreFiltered, --ignoreFiltered
      [20171031] Don't try to calculate things why variants already FILTERed 
      (faster) 
      Default: false
    -M, --max-fisher
      max inclusive value of fisher test. 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
    -m, --min-fisher
      min inclusive value of fisher test. 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
  * -p, --pedigree
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0|.|undefined|unknown:unknown;1|male|M:male;2|female|F:female), 
      phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    -Q, --qual
      Overwrite QUAL column with the lowest fisher value.
      Default: false
    --report
      [20190418] save report as bed file
    --version
      print version and exit