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bwa_and_gatk_wdl.json
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{
"#splitting_bed_file":"splitting using gatk tools SplitIntervals",
"splitting.gatk":"/home/pklab/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar",
"splitting.bed":"/data/lists/intervals.txt",
"splitting.scatter_count":10,
"splitting.refFasta":"/home/pklab/genome/hg38/hg38.fa",
"splitting.refIndex":"/home/pklab/genome/hg38/hg38.fa.fai",
"splitting.refDict":"/home/pklab/genome/hg38/hg38.dict",
"splitting.refAMB":"/home/pklab/genome/hg38/hg38.fa.amb",
"splitting.refANN":"/home/pklab/genome/hg38/hg38.fa.ann",
"splitting.refBWT":"/home/pklab/genome/hg38/hg38.fa.bwt",
"splitting.refPAC":"/home/pklab/genome/hg38/hg38.fa.pac",
"splitting.refSA":"/home/pklab/genome/hg38/hg38.fa.sa",
"#-----------------------":"-------------------------------------------------------------",
"#data_processing":"Quality Check, adapter trimming, alignment, metrics, mark dup and baserecalibration",
"data_processing.SCATTER_CALLING_INTERVALS_LIST":"/data/lists/intervals.txt",
"data_processing.FASTQ_LIST":"/data/lists/fastq_list.txt",
"data_processing.fastqc":"/home/pklab/software/FastQC/fastqc",
"data_processing.cutadapt":"/home/pklab/.local/bin/cutadapt",
"data_processing.adapters":"/data/lists/adapters.txt",
"data_processing.bwa":"/home/pklab/software/bwa/bwa",
"data_processing.samtools":"/home/pklab/software/samtools-1.8/samtools",
"data_processing.gatk":"/home/pklab/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar",
"data_processing.refFasta":"/home/pklab/genome/hg38/hg38.fa",
"data_processing.refIndex":"/home/pklab/genome/hg38/hg38.fa.fai",
"data_processing.refDict":"/home/pklab/genome/hg38/hg38.dict",
"data_processing.refAMB":"/home/pklab/genome/hg38/hg38.fa.amb",
"data_processing.refANN":"/home/pklab/genome/hg38/hg38.fa.ann",
"data_processing.refBWT":"/home/pklab/genome/hg38/hg38.fa.bwt",
"data_processing.refPAC":"/home/pklab/genome/hg38/hg38.fa.pac",
"data_processing.refSA":"/home/pklab/genome/hg38/hg38.fa.sa",
"data_processing.dbsnp38":"/home/pklab/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz",
"data_processing.dbsnp38_index":"/home/pklab/resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi",
"data_processing.phase1snps":"/home/pklab/resources/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"data_processing.phase1snps_index":"/home/pklab/resources/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"data_processing.mills":"/home/pklab/resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"data_processing.mills_index":"/home/pklab/resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"#--------------------":"----------------------------------------------------------------",
"#Mutect2_variant_calling":"Mutect2 - gatk",
"mutect_variant_calling.BAM_LIST":"/data/lists/bam_list.txt",
"mutect_variant_calling.SCATTER_CALLING_INTERVALS_LIST":"/data/lists/intervals.txt",
"mutect_variant_calling.samples":"/data/lists/samples.txt",
"mutect_variant_calling.tumor":"/data/lists/tumor.txt",
"mutect_variant_calling.normal":"/data/lists/normal.txt",
"mutect_variant_calling.refFasta":"/home/pklab/genome/hg38/hg38.fa",
"mutect_variant_calling.refIndex":"/home/pklab/genome/hg38/hg38.fa.fai",
"mutect_variant_calling.refDict":"/home/pklab/genome/hg38/hg38.dict",
"mutect_variant_calling.samtools":"/home/pklab/software/samtools-1.8/samtools",
"mutect_variant_calling.gatk":"/home/pklab/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar",
"#--------VCFs------------------":"-------------------------------------------",
"mergevcfs.VCF_samples_lists":"/data/lists/vcfs_samples_lists.txt",
"#-------_VCFs_------------------":"-------------------------------------------",
"mergevcfs.gatk":"/home/pklab/software/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar",
"mergevcfs.tabix":"/home/pklab/software/tabix/tabix",
"mergevcfs.samtools":"/home/pklab/software/samtools-1.8/samtools",
"mergevcfs.refFasta":"/home/pklab/genome/hg38/hg38.fa",
"mergevcfs.refIndex":"/home/pklab/genome/hg38/hg38.fa.fai",
"mergevcfs.refDict":"/home/pklab/genome/hg38/hg38.dict",
"##-------------------":"----------------------------------------------------------------"
}