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Meaning of terms in output of GenotypeConcordance

blueskypyblueskypy Posts: 228Member
edited October 2013 in Ask the GATK team

Just to make sure my understanding is correct:

HET: heterozygous
HOM_REF: homozygous reference
HOM_VAR: homozygous variant
MIXED: something like `./1`
Mismatching_Alleles: ??
UNAVAILABLE: for internal use
ALLELES_MATCH: ??
ALLELES_DO_NOT_MATCH: ??
EVAL_ONLY: ??
TRUTH_ONLY: does it actually mean the variants present in comp but not in eval, like COMP_ONLY?

how does the following computed?

Non-Reference_Discrepancy
Non-Reference_Sensitivity  
Overall_Genotype_Concordance

Thanks a lot!

Post edited by blueskypy on

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