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parameters.csv
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defaultInterpreter,#!/bin/bash
stage,module load
targetedInsertSize,200
checkStage,module list
### References versions ###
refExaCVersion,0.3
refGonLVersion,release5_noContam_noChildren_with_AN_AC_GTC_stripped
refGnomADExomesVersion,2.1.1
refGnomADGenomesVersion,r2.0.2
refClinvarVersion,20180401
gavinDataDir,${dataDir}/GAVIN/bundle_r1.2/
gavinCGD,${gavinDataDir}/CGD_26jun2018.txt.gz
gavinFDR,${gavinDataDir}/FDR_allGenes_r1.2.tsv
gavinCalibrations,${gavinDataDir}/GAVIN_calibrations_r0.5.tsv
gavinClinVar,${gavinDataDir}/clinvar.vkgl.patho.26june2018.vcf.gz (https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/)
### Tool versions ####
javaSuffix,Java-8-LTS
javaVersion,Java/8-LTS
hpoVersion,90
vepDBVersion,92
vepAssemblyVersion,GRCh37
bcfToolsVersion,BCFtools/1.16-${toolChain_min}
bedToolsVersion,BEDTools/2.30.0-${toolChain_min}
bwaVersion,BWA/0.7.17-20220923-139f68f-${toolChain_min}
computeVersion,Molgenis-Compute/20.03.1-Java-11-LTS
caddVersion,CADD/v1.4-foss-2018b
fastqcVersion,FastQC/0.11.9-${javaSuffix}
gatkVersion,GATK/4.2.4.1-${javaSuffix}
gatkJar,gatk-package-local.jar
gavinPlusJar,gavin-plus-RELEASE.jar
gavinPlusVersion,gavin-plus/1.5.0-${javaSuffix}
gVCF2BEDVersion,gVCF2BED/1.0.0-${toolChain_min}
jqVersion,jq/1.6
refGnomADExomesVersion,2.1.1
refGnomADGenomesVersion,r2.0.2
htsLibVersion,HTSlib/1.16-${toolChain_min}
iolibVersion,io_lib/1.14.11-${toolChain_min}
mantaVersion,manta/1.6.0-${toolChain_min}
multiQCVersion,multiqc/1.12-${toolChain_min}
ngsUtilsVersion,ngs-utils/23.04.1
picardVersion,picard/2.26.10-${javaSuffix}
pigzVersion,pigz/2.7-${toolChain_min}
python2Version,Python/2.7.16-GCCcore-7.3.0-bare
pythonVersion,Python/3.10.4-${toolChain_min}-bare
rVersion,R/4.2.1-${toolChain_max}-bare
sambambaVersion,sambamba/0.7.0
samtoolsVersion,SAMtools/1.16.1-${toolChain_min}
seqTkVersion,seqtk/1.3-${toolChain_min}
snpEffVersion,snpEff/4.3t-${javaSuffix}
vcfAnnoVersion,vcfanno/v0.3.3
vcfAnnoExecutable,vcfanno
vcfPedVersion,VCFped/20180527_d1bbdf5-foss-2018b-Python-2.7.16
##### GENERAL DIRECTORIES #####
dataDir,${appsDir}/data/
softwareDir,${appsDir}/software/
sourcesDir,${appsDir}/sources/
dbSNPDir,${dataDir}/dbSNP/
dbNSFPDir,${dataDir}/dbNSFP/
inhouseIntervalsDir,${dataDir}/UMCG/
inputData,${tmpDataDir}/inputData/
hpoDir,${dataDir}/HPO/
sequenomDir,${dataDir}/Sequenom/
tmpDataDir,${groupDir}/${tmpName}/
tempDir,${tmpDataDir}/temp/
tmpDirectory,${tmpDataDir}/tmp/NGS_DNA/
logsDir,${tmpDataDir}/logs/
##### RAW DATA FILES/DIRS ####
allRawNgsTmpDataDir,${tmpDataDir}/rawdata/ngs/
allRawArrayTmpDataDir,${tmpDataDir}/rawdata/array/
rawFile,${projectRawTmpDataDir}/${filePrefix}_${barcode}
projectRawTmpDataDir,${projectDir}/rawdata/ngs/
projectRawArrayTmpDataDir,${projectDir}/rawdata/array/
#### INDEX FILES #####
indicesDir,${dataDir}/1000G/phase1
indexFileID,human_g1k_v37
indexFileIDPhiX,${indexFileID}_phiX
indexFileFastaIndex,${indicesDir}/${indexFileIDPhiX}.fasta.fai
indexFile,${indicesDir}/${indexFileIDPhiX}.fasta
indexFileDictionary,${indicesDir}/${indexFileIDPhiX}.dict
#### Prefixes ####
runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}
filePrefix,${runPrefix}_L${lane}
samplePrefix,${intermediateDir}/${externalSampleID}
projectPrefix,${intermediateDir}/${project}
#### INTERVALS ####
nameBed,captured
intervalListDir,${dataDir}/${capturingKit}/${indexFileID}/
captured,${intervalListDir}/${nameBed}
capturedIntervals,${captured}.interval_list
capturedBed,${captured}.bed
capturedBatchBed,${captured}.batch-${batchID}.bed
femaleCapturedBatchBed,${captured}.femaleY.bed
capturedIntervalsPerBase,${captured}.uniq.per_base.bed
coveragePerBaseDir,${inhouseIntervalsDir}/Diagnostics/CoveragePerBase/
coveragePerTargetDir,${inhouseIntervalsDir}/Diagnostics/CoveragePerTarget/
capturedExomeIntervals,${dataDir}/UMCG/All_Exon_v1/${indexFileID}/${nameBed}.interval_list
capturedExomeBed,${dataDir}/UMCG/All_Exon_v1/${indexFileID}/${nameBed}.bed
#### Projects ####
projectDir,${tmpDataDir}projects/NGS_DNA/${project}/${runid}
intermediateDir,${tmpDirectory}/${project}/${runid}/
projectJobsDir,${projectDir}/jobs/
projectLogsDir,${projectDir}/logs/
projectResultsDir,${projectDir}/results/
projectQcDir,${projectDir}/qc/
### Protocols 1, 2, 3 and 4 (SpikePhiX, CheckIlluminaEncoding, FastQC, BWA) ###
outputFolderFastQC,${projectResultsDir}/qc/
peEnd1BarcodeFqGz,${rawFile}_1.${rawFileExt}
peEnd2BarcodeFqGz,${rawFile}_2.${rawFileExt}
peEnd1BarcodePhiXRecodedFqGz,${intermediateDir}/${filePrefix}_${barcode}_1.phiX.recoded.${rawFileExt}
peEnd2BarcodePhiXRecodedFqGz,${intermediateDir}/${filePrefix}_${barcode}_2.phiX.recoded.${rawFileExt}
peEnd1BarcodePhiXFqGz,${intermediateDir}/${filePrefix}_${barcode}_1.phiX.${rawFileExt}
peEnd2BarcodePhiXFqGz,${intermediateDir}/${filePrefix}_${barcode}_2.phiX.${rawFileExt}
srBarcodeRecodedFqGz,${intermediateDir}/${filePrefix}_${barcode}.recoded.${rawFileExt}
srBarcodeFqGz,${rawFile}.${rawFileExt}
srBarcodeTrimmedFq,${intermediateDir}/${filePrefix}_${barcode}.trimmed.fq
bwaAlignCores,8
humanPhiXdir,${dataDir}/inSilico/humanPhiX
simulatedPhiXVariants,${humanPhiXdir}/InSilicoData.chrNC_001422.1.variant.calls.vcf
inSilicoConcordanceFile,${intermediateDir}/inSilicoConcordance.txt
rawFileExt,fq.gz
phiXPrefix,171027_WGSIM_0000_ZZZZZZZZ
phiXEnd1Gz,${humanPhiXdir}/${phiXPrefix}/${phiXPrefix}_L1_1.${rawFileExt}
phiXEnd2Gz,${humanPhiXdir}/${phiXPrefix}/${phiXPrefix}_L1_2.${rawFileExt}
chainHg19to1000GFile,/apps/data/GRC/Hg19toHumanG1kV37.chain
### Protocols 5, 6, 7, 8 and 9 (SamToBam, SortBam, MergeBam, MarkDuplicates) ###
samToBamJar,SamFormatConverter
sortSamJar,SortSam
mergeSamFilesJar,MergeSamFiles
markDuplicatesJar,MarkDuplicates
alignedSam,${fileWithIndexId}.sam
alignedBam,${fileWithIndexId}.bam
alignedSortedBam,${fileWithIndexId}.sorted.bam
alignedSortedBamIdx,${fileWithIndexId}.sorted.bam.bai
sampleMergedBam,${samplePrefix}.merged.bam
sampleMergedBai,${samplePrefix}.merged.bai
sampleMergedBamIdx,${samplePrefix}.merged.bam.bai
dedupBam,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam
dedupBamIdx,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.bai
dedupBamMetrics,${projectResultsDir}/qc/statistics/${externalSampleID}.merged.dedup.bam
dedupBamCram,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram
dedupBamCramIdx,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram.crai
dedupBamCramBam,${projectResultsDir}/alignment/${externalSampleID}.merged.dedup.bam.cram.bam
KGPhase1IndelsVcf,${indicesDir}/indels/1000G_phase1.indels.b37.vcf
KGPhase1IndelsVcfIdx,${KGPhase1IndelsVcf}.idx
MillsGoldStandardDir,${indicesDir}/Mills_and_1000G_gold_standard/
MillsGoldStandardIndelsVcf,${MillsGoldStandardDir}/1000G_phase1.indels_Mills_and_1000G_gold_standard.indels.b37.human_g1k_v37.vcf
MillsGoldStandardChr1Intervals,${MillsGoldStandardDir}/1000G_phase1.indels_Mills_and_1000G_gold_standard.indels.b37.human_g1k_v37.chr1.intervals
### Protocols 11, 12, 13 and 14 (CheckSex, Manta, CoveragePerBase, SequonomConcordanceCheck, CollectBamMetrics) ###
whichSex,${samplePrefix}.chosenSex.txt
checkSexMeanCoverage,${samplePrefix}.checkSex.filter.meancoverage.txt
capturedIntervals_nonAutoChrX,${samplePrefix}.${nameBed}.nonAutosomalChrX.interval_list
familyList,${samplePrefix}.familylist.txt
arrayMapFile,${samplePrefix}.concordance.map
sampleConcordanceFile,${samplePrefix}.concordance.ngsVSarray.txt
sequenomReport,${tmpDataDir}/rawdata/array/${project}_Sequenom_Report.txt
sequenomInfo,${sequenomDir}/Sequonome_SNPinfo.txt
collectMultipleMetricsJar,CollectMultipleMetrics
alignmentMetrics,${dedupBamMetrics}.alignment_summary_metrics
bamIndexStats,${dedupBamMetrics}.bam_index_stats
bamIndexStatsJar,BamIndexStats
flagstatMetrics,${dedupBamMetrics}.flagstat
gcBiasMetrics,${dedupBamMetrics}.gc_bias_metrics
gcBiasMetricsJar,CollectGcBiasMetrics
insertSizeMetrics,${dedupBamMetrics}.insert_size_metrics
hsMetricsJar,CalculateHsMetrics
hsMetrics,${dedupBamMetrics}.hs_metrics
hsMetricsNonAutosomalRegionChrX,${dedupBamMetrics}.nonAutosomalRegionChrX_hs_metrics
recreateInsertSizePdfR,createInsertSizePlot_c5.R
projectDellyAnnotatorOutputVcf,${samplePrefix}.delly.snpeff.hpo.vcf
collectBamMetricsPrefix,${intermediateDir}/${externalSampleID}.merged.dedup
hpoTerms,${hpoDir}/build.${hpoVersion}/ALL_SOURCES_TYPICAL_FEATURES_diseases_to_genes_to_phenotypes.txt
caddAnnotationVcf,${dataDir}/CADD/prescored/GRCh37/no_anno/whole_genome_SNVs.vcf.gz
caddUnknownIndelAnnotation,${projectPrefix}.batch-${batchID}.unknown.indels.vcf.gz
gnomADGenomesAnnotation,${dataDir}/gnomAD/release-170228/vcf/genomes/${refGnomADGenomesVersion}/
gnomADExomesAnnotation,${dataDir}/gnomAD/${refGnomADExomesVersion}/
gonlAnnotation,${dataDir}/gonl/${refGonLVersion}/
clinvarAnnotation,${dataDir}/ClinVar/clinvar_${refClinvarVersion}.vcf.gz
mantaDir,${intermediateDir}/Manta/${externalSampleID}/
wgsMetrics,${dedupBamMetrics}.wgs_metrics
### Protocols 18a 18b 18c and (gVCF VariantCalling, VariantCombine, VariantGenotyping) ###
dbSNP137Vcf,${dbSNPDir}/dbsnp_137.b37.vcf
dbSNP137VcfIdx,${dbSNP137Vcf}.idx
dbSNPExSiteAfter129Vcf,${dbSNPDir}/dbsnp_137.b37.excluding_sites_after_129.vcf
dbSNPExSiteAfter129VcfIdx,${dbSNPExSiteAfter129Vcf}.idx
sampleBatchVariantCalls,${projectResultsDir}/variants/gVCF/${externalSampleID}.batch-${batchID}.variant.calls.g.vcf.gz
sampleVariantCalls,${projectResultsDir}/variants/gVCF/${externalSampleID}.variant.calls.g.vcf.gz
sampleBatchVariantCallsIndex,${sampleBatchVariantCalls}.tbi
sampleBatchVariantCallsMaleNONPAR,${projectResultsDir}/variants/gVCF/${externalSampleID}.batch-${batchID}.chrX.male.NONPAR.variant.calls.g.vcf.gz
sampleBatchVariantCallsMaleNONPARIndex,${sampleBatchVariantCallsMaleNONPAR}.tbi
sampleMergedBatchVariantCalls,${projectResultsDir}/variants/gVCF/${externalSampleID}.merged.variant.calls.g.vcf.gz
sampleGvcf2Bed,${projectResultsDir}/variants/gVCF/${externalSampleID}.gvcfto.bed
sampleBatchVariantCallsCompressed,${intermediateDir}/gVCF/${externalSampleID}.batch-${batchID}.variant.calls.g.vcf.gz
projectBatchCombinedVariantCalls,${projectPrefix}.batch-${batchID}.variant.calls.combined.g.vcf.gz
sampleBatchGenotypedVariantCalls,${intermediateDir}/${externalSampleID}.batch-${batchID}.variant.calls.genotyped.vcf.gz
projectBatchGenotypedVariantCalls,${projectPrefix}.batch-${batchID}.variant.calls.genotyped.vcf
sampleGenotypedVariantCalls,${intermediateDir}/${externalSampleID}.variant.calls.genotyped.vcf.gz
#annotate vcf
vcfAnnoGnomadGenomesConfSample,${samplePrefix}.conf.gnomad.genomes.txt
vcfAnnoConfSample,${samplePrefix}.conf.toml
vcfAnnoCustomConfLua,${projectPrefix}.batch-${batchID}.custom.conf.lua
vcfAnnoCustomConfLuaSample,${samplePrefix}.custom.conf.lua
vcfAnnoConf,${projectPrefix}.batch-${batchID}.conf.toml
vcfAnnoGnomadGenomesConf,${projectPrefix}.batch-${batchID}.conf.gnomad.genomes.txt
vcfAnnoGnomadExomesConf,${projectPrefix}.batch-${batchID}.conf.gnomad.exomes.txt
projectBatchGenotypedAnnotatedVariantCalls,${projectPrefix}.batch-${batchID}.variant.calls.genotyped.annotated.vcf
toCADD,${projectPrefix}.batch-${batchID}.toCadd.vcf
fromCADD,${projectPrefix}.batch-${batchID}.fromCadd.tsv.gz
fromCADDMerged,${projectPrefix}.batch-${batchID}.fromCadd.merged.vcf
#perSample
toCaddSample,${samplePrefix}.toCadd.vcf
fromCaddSample,${samplePrefix}.fromCadd.tsv.gz
sampleGenotypedAnnotatedVariantCalls,${samplePrefix}.variant.calls.genotyped.annotated.vcf
### Protocols 19, 20, 21, 21, 22, 23 and 24 (SnpEff,CmdLineAnnotator, VariantAnnotator, MergeBatches,Gavin VariantFiltration, IndelFiltration, SplitIndelsSNPs) ###
#persample
sampleVariantCallsSnpEff_Annotated,${samplePrefix}.variant.calls.snpeff.vcf
sampleVariantCallsSnpEff_SummaryHtml,${samplePrefix}.variant.calls.snpeff_Summary.html
sampleSnpsOnlyVcf,${samplePrefix}.snps.vcf
sampleIndelsOnlyVcf,${samplePrefix}.indels.vcf
projectVariantCallsSnpEff_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.snpeff.vcf
projectVariantCallsSnpEff_HPO_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.HPO.vcf
projectVariantCallsSnpEff_SummaryHtml,${projectPrefix}.batch-${batchID}.variant.calls.snpeff_Summary.html
projectVariantCallsSnpEff_ExAC_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.snpeff.exac.vcf
projectVariantCallsSnpEff_ExAC_GoNL_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.snpeff.exac.gonl.vcf
projectVariantCallsSnpEff_ExAC_GoNL_CADD_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.snpeff.exac.gonl.cadd.vcf
projectVariantCallsSnpEff_ExAC_GoNL_CADD_GATK_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.snpeff.exac.gonl.cadd.gatk.vcf
sampleVariantsMergedIndelsVcf,${samplePrefix}.annotated.indels.vcf
sampleVariantsMergedSnpsVcf,${samplePrefix}.annotated.snps.vcf
projectVariantsMerged,${projectPrefix}.variant.calls.GATK.vcf
projectVariantsIndelsOnlyVcf,${projectPrefix}.annotated.indels.vcf
projectVariantsSnpsOnlyVcf,${projectPrefix}.annotated.snps.vcf
projectVariantsMergedIdx,${projectPrefix}.variant.calls.GATK.vcf.idx
projectVariantsMergedSorted,${projectPrefix}.variant.calls.GATK.sorted.vcf
projectVariantsMergedSortedGz,${projectPrefix}.variant.calls.GATK.sorted.vcf.gz
projectVariantsMergedSortedSorted,${projectPrefix}.variant.calls.GATK.sorted.sorted.vcf
sortVCFpl,sortVCFbyFai.pl
gavinDataDir,${dataDir}/GAVIN/bundle_r1.2/
gavinCGD,${gavinDataDir}/CGD_26jun2018.txt.gz
gavinFDR,${gavinDataDir}/FDR_allGenes_r1.2.tsv
gavinCalibrations,${gavinDataDir}/GAVIN_calibrations_r0.5.tsv
gavinClinVar,${gavinDataDir}/clinvar.vkgl.patho.26june2018.vcf.gz
gavinOutputFirstPass,${samplePrefix}.GAVIN.RVCF.firstpass.vcf
gavinOutputFinal,${samplePrefix}.GAVIN.RVCF.final.vcf
gavinToCADD,${samplePrefix}.GAVIN.toCadd.tsv
gavinFromCADD,${samplePrefix}.GAVIN.fromCadd.tsv
gavinToCADDgz,${samplePrefix}.GAVIN.toCadd.tsv.gz
gavinFromCADDgz,${samplePrefix}.GAVIN.fromCadd.tsv.gz
gavinOutputFinalMerged,${samplePrefix}.GAVIN.RVCF.final.mergedWithOriginal.vcf
gavinOutputFinalMergedRLV,${samplePrefix}.GAVIN.rlv.vcf
sampleVariantsMergedGavin,${samplePrefix}.variant.calls.GATK.vcf
projectVariantCallsVEP_Annotated,${projectPrefix}.batch-${batchID}.variant.calls.VEP.vcf
### 25, 26
sampleIndelsOnlyFilteredVcf,${samplePrefix}.annotated.filtered.indels.vcf
sampleSnpsOnlyFilteredVcf,${samplePrefix}.annotated.filtered.snps.vcf
projectVariantsIndelsOnlyFilteredVcf,${projectPrefix}.annotated.filtered.indels.vcf
projectVariantsSnpsOnlyFilteredVcf,${projectPrefix}.annotated.filtered.snps.vcf
sampleFinalVcf,${intermediateDir}/${externalSampleID}.final.vcf
projectFinalVcf,${projectPrefix}.final.vcf
### Protocols 24 and 25 (VcfToTable, QCReport) ###
variantsFinalProjectVcfTable,${projectFinalVcf}.table
vcf2Table,vcf2tabV3.pl
getStatisticsScript,getStatistics.R
getDedupInfoScript,getDedupInfo.R
qcStatisticsCsv,${projectQcDir}/${project}_QCStatistics.csv
qcStatisticsTex,${projectQcDir}/${project}_QCStatistics.tex
qcStatisticsDescription,${projectQcDir}/${project}_qcstatisticsdescription.tex
qcDedupMetricsOut,${projectQcDir}/${project}_dedupmetrics.txt
qcBaitSet,${projectQcDir}/projectbaitset.txt
qcStatisticsTexReport,${projectQcDir}/${project}_QCReport.tex
qcReportMD,${projectQcDir}/${project}_QCReport.md
NGS_DNAVersionFile,${intermediateDir}/NGS_DNA-Version.txt
qcReportHtml,${projectQcDir}/${project}_QCReport.html
qcReportPdf,${projectQcDir}/${project}_QCReport.pdf
qcMetrics,${intermediateDir}/${externalSampleID}.total.qc.metrics.table
allMetrics,${intermediateDir}/${project}_qc.metricsList
multiqcDataDir,${intermediateDir}/multiqc_data
runDateInfoFile,${multiqcDataDir}/${project}.run_date_info.csv
### 5GPM Protocols (FilterOnIntervalList) ###
fileWithIndexId,${intermediateDir}/${filePrefix}_${barcode}
noExtension,variant.calls.genotyped.vcf
annotatedExtension,variant.calls.snpeff.exac.gonl.cadd.vcf
annotatedSnpEffExtension,variant.calls.snpeff.vcf
annotatedVEPExtension,variant.calls.VEP.vcf
sampleConcordanceFile,${intermediateDir}/${externalSampleID}.ConcordanceFile.txt
arrayTmpMap,${intermediateDir}/${externalSampleID}.concordance.tmp.map
arrayMapFile,${intermediateDir}/${externalSampleID}.concordance.map
familyList,${intermediateDir}/${externalSampleID}.familyList.txt
mergedBamRecalibratedTable,${projectResultsDir}/alignment/${externalSampleID}.recalibrated.table
cgdDataDir,${dataDir}/CGD/
projectBatchGenotypedCGDAnnotatedVariantCalls,${projectPrefix}.batch-${batchID}.variant.calls.genotyped.cgd.annotated.vcf
cgdFile,${cgdDataDir}/CGD_perPosition.bed.gz
sampleMergedRecalibratedBam,${samplePrefix}.merged.recalibrated.bam
sampleMergedRecalibratedBamIdx,${samplePrefix}.merged.recalibrated.bam.bai
sampleDragenVariantCalls,${samplePrefix}.variant.calls.genotyped.vcf.gz
sampleDragenRawVariantCalls,${samplePrefix}.hard-filtered.g.vcf.gz
noMerge,no
yesMerge,yes
concordanceCheckSnps,${dataDir}/UMCG/concordanceCheckSnps.bed
concordanceCheckCallsVcf,${samplePrefix}.concordanceCheckCalls.vcf
concordanceCheckCallsVcfInputGVCF,${intermediateDir}/${externalSampleID}.merged.g.vcf.gz