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Updated UnifiedGenotyper GATKDoc (note on ploidy model)

This commit is contained in:
Geraldine Van der Auwera 2013-02-04 14:17:05 -05:00
parent 41a030f4b7
commit 43e3a040b6
1 changed files with 6 additions and 5 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -82,6 +82,7 @@ import java.util.*;
* genotype of each sample. The system can either emit just the variant sites or complete genotypes (which includes
* homozygous reference calls) satisfying some phred-scaled confidence value. The genotyper can make accurate calls on
* both single sample data and multi-sample data.
* </p>
*
* <h2>Input</h2>
* <p>
@ -109,7 +110,7 @@ import java.util.*;
*
* <p>
* The above command will call all of the samples in your provided BAM files [-I arguments] together and produce a VCF file
* with sites and genotypes for all samples. The easiest way to get the dbSNP file is from the GATK resource bundle. Several
* with sites and genotypes for all samples. The easiest way to get the dbSNP file is from the GATK resource bundle (see Guide FAQs for details). Several
* arguments have parameters that should be chosen based on the average coverage per sample in your data. See the detailed
* argument descriptions below.
* </p>
@ -132,7 +133,7 @@ import java.util.*;
* <li>The system can be very aggressive in calling variants. In the 1000 genomes project for pilot 2 (deep coverage of ~35x)
* we expect the raw Qscore > 50 variants to contain at least ~10% FP calls. We use extensive post-calling filters to eliminate
* most of these FPs. Variant Quality Score Recalibration is a tool to perform this filtering.</li>
* <li>We only handle diploid genotypes</li>
* <li>The generalized ploidy model can be used to handle non-diploid or pooled samples (see the -ploidy argument in the table below).</li>
* </ul>
*
*/
@ -160,9 +161,9 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
/**
* If a call overlaps with a record from the provided comp track, the INFO field will be annotated
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).
* Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).
* Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public List<RodBinding<VariantContext>> comps = Collections.emptyList();