SVConcordance
Annotates variants with genotype concordance against another SV call set. This is a general-purpose workflow that can be applied to any pair of VCFs containing the same sample set. This is also a prerequisite step for genotype filtering in the recommended pipeline: genotypes are compared to calls emitted by raw callers, where low concordance can be indicative of poor quality variants. See GATK-SVConcordance for more information on methods.
The following diagram illustrates the recommended invocation order:
Inputs
output_prefix
Prefix for the output VCF, such as the cohort name. May be alphanumeric with underscores.
eval_vcf
VCF to annotate. In the recommended pipeline, this is generated in RefineComplexVariants.
truth_vcf
VCF to compare against. This should contain the same samples as eval_vcf. In the recommended pipeline, this is
generated in JoinRawCalls.
Outputs
concordance_vcf
"Eval" VCF annotated with genotype concordance.