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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.
This commit is contained in:
Khalid Shakir 2011-09-06 12:41:46 -04:00
parent 28d782b4c7
commit 0adb388dee
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -214,7 +214,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@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<String> 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<File> sampleFiles;
/**
@ -226,7 +226,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
/**
* 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<File> XLsampleFiles = new HashSet<File>(0);
/**