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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Standalone genotype concordance workflow #85

Closed b97pla closed 7 years ago

b97pla commented 7 years ago

This PR includes a qscript for running genotype concordance checks decoupled from the DNABestPracticeVariantCalling workflow. The workflow takes one or more "truth" genotype files and either one or more vcf files to evaluate or one or more bam files to call variants on (with UnifiedGenotyper) and then calculate concordance values.

In addition, functionality for indexing vcf files (with bcftools) and combining and validating vcf files is added.

b97pla commented 7 years ago

@johandahlberg if/when you have a moment, it'd be great if you can review this