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mutation_calling_input.json
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mutation_calling_input.json
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{
"mutation_calling.tumorFastq": ["/path/to/HCC4006_final.fastq", "/path/to/CALU1_combined_final.fastq"],
"mutation_calling.normalFastq": "/path/to/MOLM13_combined_final.fastq",
"mutation_calling.refGenome": {
"ref_fasta": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta",
"ref_fasta_index": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.fai",
"ref_dict": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.dict",
"ref_pac": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.pac",
"ref_sa": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.sa",
"ref_amb": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.amb",
"ref_ann": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.ann",
"ref_bwt": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Homo_sapiens_assembly19.fasta.bwt",
"ref_name": "hg19"
},
"mutation_calling.dbSNP_vcf_index": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/dbsnp_138.b37.vcf.gz.tbi",
"mutation_calling.dbSNP_vcf": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/dbsnp_138.b37.vcf.gz",
"mutation_calling.known_indels_sites_indices": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx",
"mutation_calling.known_indels_sites_VCFs": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/Mills_and_1000G_gold_standard.indels.b37.sites.vcf",
"mutation_calling.af_only_gnomad": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/af-only-gnomad.raw.sites.b37.vcf.gz",
"mutation_calling.af_only_gnomad_index": "/fh/fast/paguirigan_a/pub/ReferenceDataSets/genome_data/human/hg19/af-only-gnomad.raw.sites.b37.vcf.gz.tbi",
"mutation_calling.annovar_protocols": "refGene,knownGene,cosmic70,esp6500siv2_all,clinvar_20180603,gnomad211_exome",
"mutation_calling.annovar_operation": "g,f,f,f,f,f"
}