nft-vcf

nf-test plugin to support VCF files.

Requirements

nf-test version 0.7.0 or higher

Setup

To use this plugin you need to activate the nft-vcf plugin in your nf-test.config file:

config {
  plugins {
    load "nft-vcf@1.0.7"
  }
}

Usage

nft-vcf extends path by a vcf property that can be used to read VCF files. It returns VCF lines in String format and makes extensive use of HTSJDK.

Examples

def vcfFile = path("${outputDir}/chr20.dose.vcf.gz").vcf
assert vcfFile.chromosomes == ['20'] as Set 
assert vcfFile.sampleCount == 51
assert vcfFile.phased
assert vcfFile.variantCount == 7824
//output first chromosome
assert vcfFile.chromosome == "20"
//or
with(path(filename).vcf) {
   assert chromosomes == ['20'] as Set
   assert sampleCount == 51
   assert phased
   assert variantCount == 7824     
   //output first chromosome
   assert chromosome == "20"
}

`header`

Returns the VCF Header instance and allows you to access all available methods.

assert path("file.vcf.gz").vcf.header.getColumnCount() == 4

`summary`

Returns VCF summary attributes (chromosomes, variantCount, sampleCount, phasing status).

path("file.vcf.gz").vcf.summary

`chromosomes()`

Returns all chromosomes as a set of Strings.

path("file.vcf.gz").vcf.chromosomes == ['20'] as Set

`chromosome()`

Returns the first chromosome as a String.

path("file.vcf.gz").vcf.chromosome == '20'

`getVariant(String chromosome, String position)`

Returns a VariantContext instance and allows you to access all available methods.

path("file.vcf.gz").vcf.getVariant("chr20",123)
path("file.vcf.gz").vcf.getVariant("chr20",123).getContig()
path("file.vcf.gz").vcf.getVariant("chr20",123).getHetCount()
path("file.vcf.gz").vcf.getVariant("chr20",123).getAttribute("XX")

`variants`

Returns an array of VariantContext instances and allows you to access all available methods.

path("file.vcf.gz").vcf.variants.size()

`getVariants(int numberOflines)`

Returns an array of n VariantContext instances and allows you to access all available methods.

path("file.vcf.gz").vcf.getVariants(100).size()

`getVariantsAsStrings(int numberOflines)`

Returns a String array including n lines.

path("file.vcf.gz").vcf.getVariantsAsStrings(100).size()

`variantsMD5`

Returns the MD5 hashsum of all variants.

path("file.vcf.gz").vcf.variantsMD5

`getVariantsByRange(String chromosome, int start, int stop)`