Overview

Compare calls in two VCF files

Input

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

Output

• 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.