From 0adb388dee3abd3272dd831c76ac4fdb69769632 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Tue, 6 Sep 2011 12:41:46 -0400 Subject: [PATCH] Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue. Updates for HybridSelectionPipeline: - Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5. - If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds. - Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches. - Removed GSA_PRODUCTION_ONLY flag from indel caller. - Updated indel hard filters based on delangel's analysis. - Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now. --- .../sting/gatk/walkers/variantutils/SelectVariants.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index bb3cd82a1..35ff66243 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -214,7 +214,7 @@ public class SelectVariants extends RodWalker { @Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false) public Set sampleExpressions ; - @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false) + @Input(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line) to include. Can be specified multiple times", required=false) public Set sampleFiles; /** @@ -226,7 +226,7 @@ public class SelectVariants extends RodWalker { /** * Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded. */ - @Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false) + @Input(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false) public Set XLsampleFiles = new HashSet(0); /**