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Quick small updates: 

SelectVariants: typo
MethodsDevelopmentPipeline: Added CEU Trio WGS dataset


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5818 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-18 20:08:39 +00:00
parent b5b8cb959a
commit ebcd333ed8
2 changed files with 5 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -92,7 +92,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="selectSNPs", shortName="snps", doc="Select only SNPs.", required=false)
private boolean SELECT_SNPS = false;
@Argument(fullName="selectIndels", shortName="indels", doc="Select only SNPs.", required=false)
@Argument(fullName="selectIndels", shortName="indels", doc="Select only Indels.", required=false)
private boolean SELECT_INDELS = false;

4
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -129,6 +129,10 @@ class MethodsDevelopmentCallingPipeline extends QScript {
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, 97.0, !lowPass),
"WGSTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **