From 4093909a56ad3366308da40656cf2317b594e7ab Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 1 Aug 2012 14:30:24 -0400 Subject: [PATCH] Updating VQSR docs. Removing references to old best practices pages. --- .../sting/gatk/walkers/bqsr/BQSR.R | 1 + .../ApplyRecalibration.java | 6 ++--- .../VariantRecalibrator.java | 22 ++++--------------- 3 files changed, 7 insertions(+), 22 deletions(-) diff --git a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R b/public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R index fd301cd97..6c4dace1d 100644 --- a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R +++ b/public/R/scripts/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.R @@ -1,4 +1,5 @@ library("ggplot2") +library("tools") #For compactPDF in R 2.13+ args <- commandArgs(TRUE) data <- read.csv(args[1]) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 744a094c6..073f56707 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -58,14 +58,11 @@ import java.util.*; * to the desired level but also has the information necessary to pull out more variants for a higher sensitivity but a * slightly lower quality level. * - *

- * See the GATK wiki for a tutorial and example recalibration accuracy plots. - * *

Input

*

* The input raw variants to be recalibrated. *

- * The recalibration table file in CSV format that was generated by the VariantRecalibrator walker. + * The recalibration table file in VCF format that was generated by the VariantRecalibrator walker. *

* The tranches file that was generated by the VariantRecalibrator walker. * @@ -82,6 +79,7 @@ import java.util.*; * --ts_filter_level 99.0 \ * -tranchesFile path/to/output.tranches \ * -recalFile path/to/output.recal \ + * -mode SNP \ * -o path/to/output.recalibrated.filtered.vcf * * diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 2a424e15b..a2909d4ca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; @@ -48,7 +47,6 @@ import org.broadinstitute.sting.utils.io.Resource; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.io.FileNotFoundException; @@ -73,15 +71,9 @@ import java.util.*; * the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model. * *

- * NOTE: Please see our best practices wiki page for our recommendations on which annotations to use for specific project designs. - * - *

* NOTE: In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version). * See http://www.r-project.org for more info on how to download and install R. * - *

- * See the GATK wiki for a tutorial and example recalibration accuracy plots. - * *

Input

*

* The input raw variants to be recalibrated. @@ -90,7 +82,7 @@ import java.util.*; * *

Output

*

- * A recalibration table file in CSV format that is used by the ApplyRecalibration walker. + * A recalibration table file in VCF format that is used by the ApplyRecalibration walker. *

* A tranches file which shows various metrics of the recalibration callset as a function of making several slices through the data. * @@ -102,8 +94,9 @@ import java.util.*; * -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ * -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ * -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ - * -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf \ - * -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \ + * -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.b37.vcf \ + * -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff \ + * -mode SNP \ * -recalFile path/to/output.recal \ * -tranchesFile path/to/output.tranches \ * -rscriptFile path/to/output.plots.R @@ -187,9 +180,6 @@ public class VariantRecalibrator extends RodWalker