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VariantFiltering.inputs.json
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VariantFiltering.inputs.json
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{
"VariantFiltering_WF.genome_ref": "RefSeq.chromosomes.fa",
"VariantFiltering_WF.genome_ref_index": "RefSeq.chromosomes.fa.fai",
"VariantFiltering_WF.genome_ref_dict": "RefSeq.chromosomes.dict",
"VariantFiltering_WF.repeats": "RefSeq.chromosomes.intervals",
"VariantFiltering_WF.inputVcfFile": "variants.raw.vcf.gz",
"VariantFiltering_WF.inputVcfFileIndex": "variants.raw.vcf.gz.tbi",
"VariantFiltering_WF.basename": "basename",
"VariantFiltering_WF.onlyBiallelic": "true",
"VariantFiltering_WF.filterDPValue": "5",
"VariantFiltering_WF.filterMissingMAF": "false",
"VariantFiltering_WF.QD": "2.0",
"VariantFiltering_WF.MQ": "30.0",
"VariantFiltering_WF.FS": "100.0",
"VariantFiltering_WF.SOR": "5.0",
"VariantFiltering_WF.workDir": "workingDir",
"VariantFiltering_WF.log": "workingDir/log",
"VariantFiltering_WF.tmp": "workingDir/tmp",
"VariantFiltering_WF.filterDensityScript": "filterDensity.groovy",
"VariantFiltering_WF.calculateStatsScript": "calculate_stats_gz.sh",
"VariantFiltering_WF.calculateIStatsScript": "calculate_istats.sh",
"VariantFiltering_WF.calculateHistogramsScript": "calculate_histograms.sh",
"VariantFiltering_WF.threads": "10",
"VariantFiltering_WF.java": "/bin/java",
"VariantFiltering_WF.picard": "/bin/picard.jar",
"VariantFiltering_WF.gatk": "/bin/gatk",
"VariantFiltering_WF.tabix": "/bin/tabix",
"VariantFiltering_WF.vcftools": "/bin/vcftools",
"VariantFiltering_WF.bcftools": "/bin/bcftools",
"VariantFiltering_WF.groovy": "/bin/groovy"
}