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Further updating VQSR tutorial wiki docs to reflect the bundle

This commit is contained in:
Ryan Poplin 2011-11-29 14:00:57 -05:00
parent 447e9bff9e
commit cb284eebde
2 changed files with 2 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -76,7 +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.b37.subset.vcf \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \
* --ts_filter_level 99.0 \
* -tranchesFile path/to/output.tranches \
* -recalFile path/to/output.recal \

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -92,7 +92,7 @@ import java.util.*;
* java -Xmx4g -jar GenomeAnalysisTK.jar \
* -T VariantRecalibrator \
* -R reference/human_g1k_v37.fasta \
* -input NA12878.HiSeq.WGS.bwa.cleaned.raw.b37.subset.vcf \
* -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 \