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ATLAS / Auxiliary VCF Tools: VCFCompare


Compare calls in two VCF files


  • two VCF files to compare
  • names of the samples to compare


  • table summarizing the amount of calls for every combination of two genotypes

Usage Example

./atlas task=VCFCompare vcf=example1.vcf,example2.vcf.gz samples=nameOfSampleInExample1Vcf,nameOfSampleInExample2Vcf

Specific Arguments

  • vcf: comma-separated list of VCF file names to be compared. Currently it is only possible to provide two.
  • samples: comma-separated list of sample names in respective VCF for which calls should be compared
  • limitLines: amount of lines to be read from VCF file

Engine Parameters

Engine parameters that are common to all tasks can be found here.