Test-drive the GATK tools and Best Practices pipelines on Terra
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Genotype Concordane Question
I am using the Genotyper Concordance tool to compare the same sample processed in two different ways. The two VCF files have these samples labeled as having different IDs, and when I do a comparison I get the following output:
:GATKTable:GenotypeConcordance_Summary:Per-sample summary statistics: NRS and NRD
Sample Non-Reference Sensitivity Non-Reference Discrepancy
ALL 0.000 1.000
:GATKTable:SiteConcordance_Summary:Site-level summary statistics
ALLELES_MATCH EVAL_SUPERSET_TRUTH EVAL_SUBSET_TRUTH ALLELES_DO_NOT_MATCH EVAL_ONLY TRUTH_ONLY
51763 14 23 26 5207 34837512
Is this because the ID's do not match? Is there an option to set up a naming mapping, and why am I not getting a value for Overall_Genotype_Concordance?