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bugfix in hsMetrics + copying original vcf from DRAGEN to results folder #336

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bugfix in hsMetrics + copying original vcf from DRAGEN to results folder #336

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5bd3426
bugfix in hsMetrics + copying original vcf from DRAGEN to results folder
RoanKanninga Dec 6, 2024
16b2312
t push
RoanKanninga Dec 6, 2024
3999bbe
fixing concordanceCheckVcf header
RoanKanninga Dec 19, 2024
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3 changes: 2 additions & 1 deletion parameters.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,7 @@ sampleMergedBamIdx,${samplePrefix}.merged.bam.bai
dedupBam,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam
dedupBamIdx,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.bai
dedupBamMetrics,${projectResultsDir}/qc/statistics/${externalSampleID}.merged.dedup.bam
dedupBamChrXMetrics,${projectResultsDir}/qc/${externalSampleID}.merged.dedup.bam
dedupBamCram,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram
dedupBamCramIdx,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram.crai
dedupBamCramBam,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram.bam
Expand Down Expand Up @@ -176,7 +177,7 @@ gcBiasMetricsJar,CollectGcBiasMetrics
insertSizeMetrics,${dedupBamMetrics}.insert_size_metrics
hsMetricsJar,CalculateHsMetrics
hsMetrics,${dedupBamMetrics}.hs_metrics
hsMetricsNonAutosomalRegionChrX,${dedupBamMetrics}.nonAutosomalRegionChrX_hs_metrics
hsMetricsNonAutosomalRegionChrX,${dedupBamChrXMetrics}.nonAutosomalRegionChrX_hs_metrics
recreateInsertSizePdfR,createInsertSizePlot_c5.R
projectDellyAnnotatorOutputVcf,${samplePrefix}.delly.snpeff.hpo.vcf
collectBamMetricsPrefix,${intermediateDir}/${externalSampleID}.merged.dedup
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3 changes: 3 additions & 0 deletions protocols/PrepareDragenData.sh
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Expand Up @@ -34,6 +34,7 @@ combinedIdentifier=$(basename "${combinedIdentifier}")
echo "${combinedIdentifier}" > "${intermediateDir}/${externalSampleID}.txt"
rsync -av "${tmpDataDir}/${gsBatch}/Analysis/${combinedIdentifier}/${combinedIdentifier}.hard-filtered"*"vcf.gz"* "${intermediateDir}"


## rename (g)VCF files
rename "${combinedIdentifier}" "${externalSampleID}" "${intermediateDir}/${combinedIdentifier}.hard-filtered."*"vcf.gz"*

Expand All @@ -43,6 +44,8 @@ bgzip -c -f "${intermediateDir}/${externalSampleID}.variant.calls.genotyped.vcf.
echo "start indexing ${intermediateDir}/${externalSampleID}.variant.calls.genotyped.vcf.gz"
tabix -p vcf "${intermediateDir}/${externalSampleID}.variant.calls.genotyped.vcf.gz"

rsync -av "${intermediateDir}/${externalSampleID}.variant.calls.genotyped.vcf.gz" "${projectResultsDir}/variants/"

rename 'gvcf.gz' 'g.vcf.gz' "${intermediateDir}/${externalSampleID}.hard-filtered.gvcf.gz"*
rsync -av "${intermediateDir}/${externalSampleID}.hard-filtered.g.vcf.gz"* "${projectResultsDir}/variants/gVCF/"

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5 changes: 5 additions & 0 deletions protocols/ReheaderVCF.sh
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Expand Up @@ -13,18 +13,23 @@ set -o pipefail
#string projectResultsDir
#string capturingKit
#string dataDir
#string concordanceCheckCallsVcf

module load "${bcfToolsVersion}"
module load "${htsLibVersion}"

##new prefix will be externalSampleID + sampleProcessStepIDwith new sample identifier --> familyname+umcgnumber
newGVCFSampleIdentifier=$(echo "${externalSampleID}" | awk 'BEGIN {FS="_"}{print $1"_"$2}')

oldIdentifier=$(cat "${intermediateDir}/${externalSampleID}.txt")
echo -e "old:${oldIdentifier}, new:${newGVCFSampleIdentifier}"
echo -e "${oldIdentifier} ${newGVCFSampleIdentifier}" > "${intermediateDir}/${externalSampleID}.newVCFHeader.txt"
echo -e "${oldIdentifier} ${externalSampleID}" > "${intermediateDir}/${externalSampleID}.newConcordanceCheckHeader.txt"

echo "##intervals=[${dataDir}/${capturingKit}/human_g1k_v37/captured.merged.bed]" > "${intermediateDir}/bedfile.txt"
bcftools reheader -s "${intermediateDir}/${externalSampleID}.newVCFHeader.txt" "${gavinOutputFinalMergedRLV}.gz" -o "${gavinOutputFinalMergedRLV}.gz.tmp"
bcftools reheader -s "${intermediateDir}/${externalSampleID}.newConcordanceCheckHeader.txt" "${concordanceCheckCallsVcf}" -o "${concordanceCheckCallsVcf}.tmp"
mv "${concordanceCheckCallsVcf}.tmp" "${concordanceCheckCallsVcf}"
bcftools annotate -h "${intermediateDir}/bedfile.txt" -O v -o "${gavinOutputFinalMergedRLV}.tmp.vcf.gz" "${gavinOutputFinalMergedRLV}.gz.tmp"
mv -v "${gavinOutputFinalMergedRLV}.tmp.vcf.gz" "${gavinOutputFinalMergedRLV}.gz"
tabix -f -p vcf "${gavinOutputFinalMergedRLV}.gz"
Expand Down