Expanded documentation to include description of which callsets are being compared in what order and more definitions
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Laura Gauthier
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9be07e0838
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06d78ba068
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@ -68,49 +68,62 @@ import java.util.*;
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* <h3>Output</h3>
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* <p>
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* Genotype Concordance writes a GATK report to the specified file (via -o), consisting of multiple tables of counts
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* and proportions. These tables are constructed on a per-sample basis, and include counts of EVAL vs COMP genotype states, and the
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* number of times the alternate alleles between the EVAL and COMP sample did not match up.
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* and proportions. These tables are constructed on a per-sample basis, and include counts of EVAL vs COMP genotype
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* states.
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* </p>
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* <h4>Tables</h4>
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* <p>
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* Headers for the (non-moltenized -- see below) GenotypeConcordance counts and proportions tables give the genotype of
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* the COMP callset followed by the genotype of the EVAL callset. For example the value corresponding to HOM_REF_HET
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* reflects variants called HOM_REF in the COMP callset and HET in the EVAL callset. Variants for which the alternate
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* alleles between the EVAL and COMP sample did not match are excluded from genotype comparisons and given in the
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* "Mismatching_Alleles" field.
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* </p>
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* <p>
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* It may be informative to reshape rows of the GenotypeConcordance counts and proportions tables into separate row-major tables
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* where the columns indicate the COMP genotype and the rows indicate the EVAL genotype for easy comparison between the
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* two callsets. This can be done with a command similar to d <- matrix(sampleRow,nrow=6,byrow=T) in R where sampleRow is the 36-value row corresponding to the sample of interest, excluding "Mismatching_Alleles".
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* In Excel this can be accomplished using the OFFSET function.
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* </p>
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* <ul>
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* <li><i>GenotypeConcordance_CompProportions</i>: Gives the proportion of variants in each category normalized to the total number of called genotypes in the COMP callset</li>
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* <li><i>GenotypeConcordance_Counts</i>: Gives the counts for number of genotypes in each category</li>
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* <li><i>GenotypeConcordance_EvalProportions</i>: Gives the proportion of genotypes in each category normalized to the total number of called genotypes in the EVAL callset</li>
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* <li><i>GenotypeConcordance_Summary</i>: Summary statistics for the sum of all samples and each sample individually. See below for definitions.</li>
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* <li><i>SiteConcordance_Summary</i>: Gives comparison counts of called genotypes and their alleles between the two callsets. See below for definitions.</li>
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* </ul>
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* </p>
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*
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* <h4>Term and metrics definitions</h4>
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* <p>
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* <ul>
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* <li>HET: heterozygous</li>
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* <li>HOM_REF: homozygous reference</li>
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* <li>HOM_VAR: homozygous variant</li>
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* <li>MIXED: something like ./1</li>
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* <li>ALLELES_MATCH: counts of calls at the same site where the alleles match</li>
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* <li>ALLELES_DO_NOT_MATCH: counts of calls at the same location with different alleles, such as the eval set calling a 'G' alternate allele, and the comp set calling a 'T' alternate allele</li>
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* <li>EVAL_ONLY: counts of sites present only in the EVAL set, not in the COMP set</li>
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* <li>TRUTH_ONLY: counts of sites present only in the COMP set, not in the EVAL set</li>
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* <li>Non-Reference_Discrepancy (NRD): genotype concordance excluding concordant reference sites</li>
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* <li>Non-Reference_Sensitivity (NRS): sensitivity of the EVAL calls to polymorphic calls in the COMP set, calculated by (# true positive)/(# true polymorphic)</li>
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* <li>Overall_Genotype_Concordance: overall concordance calculated by (# concordant genotypes)/(# genotypes)</li>
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* <li><i>GenotypeConcordance_CompProportions</i>, <i>GenotypeConcordance_Counts</i>, and <i>GenotypeConcordance_EvalProportions</i></li>
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* <ul>
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* <li>NO_CALL: reported genotype is ./., indicating not enough data to call</li>
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* <li>HET: heterozygous</li>
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* <li>HOM_REF: homozygous reference</li>
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* <li>HOM_VAR: homozygous variant</li>
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* <li>UNAVAILABLE: variant is not called in this callset</li>
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* <li>MIXED: something like ./1</li>
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* </ul>
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* <li><i>GenotypeConcordance_Summary<i></li>
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* <ul>
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* <li>Non-Reference_Sensitivity (NRS): sensitivity of the EVAL calls to polymorphic calls in the COMP set, calculated by (# true positive)/(# true polymorphic)</li>
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* <li>Non-Reference_Discrepancy (NRD): genotype discordance excluding concordant reference sites, calculated by (# discordant sites)/(total excluding # HOM_REF_HOM_REF) = 1.0-(# HOM_VAR_HOM_VAR + # HET_HET)/(total excluding # HOM_REF_HOM_REF)</li>
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* <li>Overall_Genotype_Concordance: overall concordance calculated by (# concordant genotypes)/(# genotypes)</li>
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* </ul>
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* <li><i>SiteConcordance_Summary</i></li>
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* <ul>
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* <li>ALLELES_MATCH: counts of calls at the same site where the alleles match</li>
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* <li>ALLELES_DO_NOT_MATCH: counts of calls at the same location with different alleles, such as the EVAL set calling a 'G' alternate allele, and the comp set calling a 'T' alternate allele</li>
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* <li>EVAL_SUBSET_TRUTH: (multi-alleleic sites only) ALT alleles for EVAL are a subset of ALT alleles for COMP. See also below.</li>
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* <li>EVAL_SUPERSET_TRUTH: (multi-allelic sites only) ALT alleles for COMP are a subset of ALT alleles for EVAL. See also below.</li>
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* <li>EVAL_ONLY: counts of sites present only in the EVAL set, not in the COMP set</li>
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* <li>TRUTH_ONLY: counts of sites present only in the COMP set, not in the EVAL set</li>
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* </ul>
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* </ul>
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* </p>
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*
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* <h4>Moltenized tables</h4>
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*
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* <p>These tables may be optionally moltenized via the -moltenize argument. That is, the standard table
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*
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* <pre>
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* Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR (...)
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* NA12878 0.003 0.001 0.000 (...)
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* NA12891 0.005 0.000 0.000 (...)
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* </pre>
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*
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* would instead be displayed
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*
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* <pre>
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* NA12878 NO_CALL_HOM_REF 0.003
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* NA12878 NO_CALL_HET 0.001
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* NA12878 NO_CALL_HOM_VAR 0.000
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* NA12891 NO_CALL_HOM_REF 0.005
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* NA12891 NO_CALL_HET 0.000
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* NA12891 NO_CALL_HOM_VAR 0.000
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* (...)
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* </pre>
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*
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* <h4>Site-level allelic concordance</h4>
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*
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* <p>
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@ -158,6 +171,27 @@ import java.util.*;
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* in which case all records are used. There is currently no way to assess concordance metrics on filtered sites
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* exclusively. SelectVariants can be used to extract filtered sites, and VariantFiltration used to un-filter them.
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*
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* <h4>Moltenized tables</h4>
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*
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* <p>These tables may be optionally moltenized via the -moltenize argument. That is, the standard table
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*
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* <pre>
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* Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR (...)
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* NA12878 0.003 0.001 0.000 (...)
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* NA12891 0.005 0.000 0.000 (...)
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* </pre>
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*
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* would instead be displayed
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*
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* <pre>
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* NA12878 NO_CALL_HOM_REF 0.003
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* NA12878 NO_CALL_HET 0.001
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* NA12878 NO_CALL_HOM_VAR 0.000
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* NA12891 NO_CALL_HOM_REF 0.005
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* NA12891 NO_CALL_HET 0.000
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* NA12891 NO_CALL_HOM_VAR 0.000
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* (...)
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* </pre>
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*/
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@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
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