zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Extend the documentation of GenotypeConcordance to include notes about Monomorphic and Filtered VCF records. 

Address Geraldine's comments - information on moltenization and explanation of fields

Fix paren
This commit is contained in:
Chris Hartl 2013-06-12 13:54:30 -04:00
parent 28a8d74290
commit af275fdf10
1 changed files with 51 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
View File

@ -67,8 +67,58 @@ import java.util.*;
*
* <h3>Output</h3>
* Genotype Concordance writes a GATK report to the specified file (via -o) , consisting of multiple tables of counts
* and proportions. These tables may be optionally moltenized via the -moltenize argument.
* and proportions. These tables may be optionally moltenized via the -moltenize argument. That is, the standard table
*
* Sample NO_CALL_HOM_REF NO_CALL_HET NO_CALL_HOM_VAR (...)
* NA12878 0.003 0.001 0.000 (...)
* NA12891 0.005 0.000 0.000 (...)
*
* would instead be displayed
*
* NA12878 NO_CALL_HOM_REF 0.003
* NA12878 NO_CALL_HET 0.001
* NA12878 NO_CALL_HOM_VAR 0.000
* NA12891 NO_CALL_HOM_REF 0.005
* NA12891 NO_CALL_HET 0.000
* NA12891 NO_CALL_HOM_VAR 0.000
* (...)
*
*
* These tables are constructed on a per-sample basis, and include counts of eval vs comp genotype states, and the
* number of times the alternate alleles between the eval and comp sample did not match up.
*
* In addition, Genotype Concordance produces site-level allelic concordance. For strictly bi-allelic VCFs,
* only the ALLELES_MATCH, EVAL_ONLY, TRUTH_ONLY fields will be populated, but where multi-allelic sites are involved
* counts for EVAL_SUBSET_TRUTH and EVAL_SUPERSET_TRUTH will be generated.
*
* For example, in the following situation
* eval: ref - A alt - C
* comp: ref - A alt - C,T
* then the site is tabulated as EVAL_SUBSET_TRUTH. Were the situation reversed, it would be EVAL_SUPERSET_TRUTH.
* However, in the case where eval has both C and T alternate alleles, both must be observed in the genotypes
* (that is, there must be at least one of (0/1,1/1) and at least one of (0/2,1/2,2/2) in the genotype field). If
* one of the alleles has no observations in the genotype fields of the eval, the site-level concordance is
* tabulated as though that allele were not present in the record.
*
* <h3>Monomorphic Records</h3>
* A site which has an alternate allele, but which is monomorphic in samples, is treated as not having been
* discovered, and will be recorded in the TRUTH_ONLY column (if a record exists in the comp VCF), or not at all
* (if no record exists in the comp VCF).
*
* That is, in the situation
* eval: ref - A alt - C genotypes - 0/0 0/0 0/0 ... 0/0
* comp: ref - A alt - C ... 0/0 0/0 ...
* is equivalent to
* eval: ref - A alt - . genotypes - 0/0 0/0 0/0 ... 0/0
* comp: ref - A alt - C ... 0/0 0/0 ...
*
* When a record is present in the comp VCF the *genotypes* for the monomorphic site will still be used to evaluate
* per-sample genotype concordance counts.
*
* <h3>Filtered Records</h3>
* Filtered records are treated as though they were not present in the VCF, unless -ignoreSiteFilters is provided,
* in which case all records are used. There is currently no way to assess concordance metrics on filtered sites
* exclusively. SelectVariants can be used to extract filtered sites, and VariantFiltration used to un-filter them.
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class GenotypeConcordance extends RodWalker<List<Pair<VariantContext,VariantContext>>,ConcordanceMetrics> {