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
./atlas task=VCFCompare vcf=example1.vcf,example2.vcf.gz samples=nameOfSampleInExample1Vcf,nameOfSampleInExample2Vcf
- 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 that are common to all tasks can be found here.