Merge pull request #329 from RoanKanninga/master

fixing concordancecheckgenotyping

README.md

@@ -20,4 +20,3 @@ Based on quality thresholds from the GATK "best practices"<sup>5</sup>, the SNPs
 3. Tarasov A et al. (2015). Sambamba: Fast processing of NGS alignment formats.<br/>
 4. McKenna A et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.<br/>
 5. Van der Auwera GA et al. (2013). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.<br/>
-

parameters.csv

@@ -322,4 +322,5 @@ sampleDragenRawVariantCalls,${samplePrefix}.hard-filtered.g.vcf.gz
 noMerge,no
 yesMerge,yes
 concordanceCheckSnps,${dataDir}/UMCG/concordanceCheckSnps.bed
-concordanceCheckCallsVcf,${samplePrefix}.concordanceCheckCalls.vcf
+concordanceCheckCallsVcf,${samplePrefix}.concordanceCheckCalls.vcf
+concordanceCheckCallsVcfInputGVCF,${intermediateDir}/${externalSampleID}.merged.g.vcf.gz

protocols/ConcordanceCheckGenotyping.sh

@@ -13,6 +13,7 @@ set -o pipefail
 #string externalSampleID
 #string concordanceCheckSnps
 #string concordanceCheckCallsVcf
+#string inputGVCF
 
 #Function to check if array contains value
 
@@ -24,17 +25,17 @@ module purge
 module load "${gatkVersion}"
 module list
 
-if [[ -f "${intermediateDir}/${externalSampleID}.merged.g.vcf.gz" ]]
+if [[ -f "${inputGVCF}" ]]
 then
 	gatk --java-options "-Xmx7g -XX:ParallelGCThreads=2 -Djava.io.tmpdir=${tempDir}" GenotypeGVCFs \
 	-R "${indexFile}" \
-	--variant "${intermediateDir}/${externalSampleID}.merged.g.vcf.gz" \
+	--variant "${inputGVCF}" \
 	--include-non-variant-sites true \
 	-L "${concordanceCheckSnps}" \
 	-O "${tmpConcordanceCheckCallsVcf}"
 
 	mv -v "${tmpConcordanceCheckCallsVcf}" "${concordanceCheckCallsVcf}"
 
 else
-	echo "The ${intermediateDir}/${externalSampleID}.merged.g.vcf.gz does not exist"
+	echo "The ${inputGVCF} does not exist"
 fi

workflow.csv

@@ -21,7 +21,7 @@ s14b_CombineGVCFs,protocols/CombineGVCFs.sh,s14a_VariantCalling
 s14c_GenotypeVariants,protocols/VariantGenotyping.sh,s14b_CombineGVCFs;dbSnp=dbSNP137Vcf
 s15_CoverageCalculationsGvcf,protocols/CoverageCalculations_gvcf.sh,s14c_GenotypeVariants;variantCalls=sampleMergedBatchVariantCalls;merge=yesMerge
 s16_AnnotateVcf,protocols/AnnotateVcf.sh,s14c_GenotypeVariants
-s17_ConcordanceCheckGenotyping,protocols/ConcordanceCheckGenotyping.sh,s15_CoverageCalculationsGvcf
+s17_ConcordanceCheckGenotyping,protocols/ConcordanceCheckGenotyping.sh,s15_CoverageCalculationsGvcf;inputGVCF=concordanceCheckCallsVcfInputGVCF
 s18_SnpEff,protocols/SnpEff.sh,s16_AnnotateVcf
 s19_MergeBatches,protocols/MergeBatches.sh,s18_SnpEff;extension=annotatedSnpEffExtension
 s20_SplitIndelsAndSNPs,protocols/SplitIndelsAndSNPs.sh,s19_MergeBatches

workflow_DRAGEN.csv

@@ -4,7 +4,7 @@ s02_ProcessDragenTrendAnalysis,protocols/ProcessDragenTrendAnalysis.sh,s01_Prepa
 s03_CoverageCalculations,protocols/CoverageCalculations_gvcf.sh,s01_PrepareDragenData;variantCalls=sampleDragenRawVariantCalls;merge=noMerge
 s04_AnnotateVcf,protocols/AnnotateVcf_perSample.sh,s01_PrepareDragenData;variantCalls=sampleDragenVariantCalls
 s05_SnpEff,protocols/SnpEff_perSample.sh,s04_AnnotateVcf
-s06_ConcordanceCheckGenotyping,protocols/ConcordanceCheckGenotyping.sh,s03_CoverageCalculations
+s06_ConcordanceCheckGenotyping,protocols/ConcordanceCheckGenotyping.sh,s03_CoverageCalculations;inputGVCF=sampleDragenRawVariantCalls
 s08_Gavin,protocols/Gavin.sh,s05_SnpEff;inputFile=sampleVariantCallsSnpEff_Annotated
 s09_ReheaderVcf,protocols/ReheaderVCF.sh,s08_Gavin
 s10_PipelineFinished,protocols/PipelineFinished.sh,s02_ProcessDragenTrendAnalysis;s06_ConcordanceCheckGenotyping;s09_ReheaderVcf