From 43e3a040b6f09569549c892920e4b07e66148d93 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Mon, 4 Feb 2013 14:17:05 -0500 Subject: [PATCH] Updated UnifiedGenotyper GATKDoc (note on ploidy model) --- .../gatk/walkers/genotyper/UnifiedGenotyper.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index d16ece4fd..c6284852e 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -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. + *

* *

Input

*

@@ -109,7 +110,7 @@ import java.util.*; * *

* 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. *

@@ -132,7 +133,7 @@ import java.util.*; *
  • 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.
    • - *
  • We only handle diploid genotypes
    • + *
  • The generalized ploidy model can be used to handle non-diploid or pooled samples (see the -ploidy argument in the table below).
    • * * */ @@ -160,9 +161,9 @@ public class UnifiedGenotyper extends LocusWalker, 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> comps = Collections.emptyList();