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Updating VQSR tutorial wiki docs to reflect the bundle

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Ryan Poplin 2011-11-29 09:57:45 -05:00
parent 75d93e6335
commit 447e9bff9e
2 changed files with 9 additions and 8 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -57,8 +57,7 @@ import java.util.*;
* slightly lower quality level.
*
* <p>
* See the GATK wiki for a tutorial and example recalibration accuracy plots.
* http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration
* See <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration">the GATK wiki for a tutorial and example recalibration accuracy plots.</a>
*
* <h2>Input</h2>
* <p>
@ -77,7 +76,7 @@ import java.util.*;
* java -Xmx3g -jar GenomeAnalysisTK.jar \
* -T ApplyRecalibration \
* -R reference/human_g1k_v37.fasta \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.hg19.subset.vcf \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.b37.subset.vcf \
* --ts_filter_level 99.0 \
* -tranchesFile path/to/output.tranches \
* -recalFile path/to/output.recal \

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -66,12 +66,14 @@ import java.util.*;
* the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.
*
* <p>
* NOTE: Please see our <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3">best practices wiki page</a> for our recommendations on which annotations to use for specific project designs.
*
* <p>
* 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 <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
*
* <p>
* See the GATK wiki for a tutorial and example recalibration accuracy plots.
* http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration
* See <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration">the GATK wiki for a tutorial and example recalibration accuracy plots.</a>
*
* <h2>Input</h2>
* <p>
@ -83,18 +85,18 @@ import java.util.*;
* <p>
* A recalibration table file in CSV format that is used by the ApplyRecalibration walker.
* <p>
* A tranches file which shows various metrics of the recalibration callset as a function of making several slices through the data.
* A tranches file which shows various metrics of the recalibration callset as a function of making several slices through the data.
*
* <h2>Example</h2>
* <pre>
* java -Xmx4g -jar GenomeAnalysisTK.jar \
* -T VariantRecalibrator \
* -R reference/human_g1k_v37.fasta \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.hg19.subset.vcf \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.b37.subset.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 FS -an MQ \
* -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \
* -recalFile path/to/output.recal \
* -tranchesFile path/to/output.tranches \
* -rscriptFile path/to/output.plots.R