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config.yaml
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SAMPLES: "samples.tsv"
GENOME: "/rds/project/rds-O11U8YqSuCk/SM/annotations/gatkresources/Homo_sapiens_assembly38.fasta"
GTF: "/rds/project/yhbl2/rds-yhbl2-genehunter/SM/annotations/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
DBSNP: "/rds/project/rds-O11U8YqSuCk/SM/annotations/gatkresources/Homo_sapiens_assembly38.dbsnp138.vcf"
INDELS: "/rds/project/rds-O11U8YqSuCk/SM/annotations/gatkresources/Homo_sapiens_assembly38.known_indels.vcf"
GOLD_STANDARD: "/rds/project/rds-O11U8YqSuCk/SM/annotations/gatkresources/Mills_and_1000G_gold_standard.indels.hg38.vcf"
INDEX: "/rds/project/rds-O11U8YqSuCk/SM/annotations/StarGRCh38Index"
ADAPTERS: "CTGTAGGCACCATCAAT"
PAIRED: 'TRUE'
GNOMAD: "/rds/project/rds-O11U8YqSuCk/SM/annotations/GNOMAD/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf"
GNOMAD_BIALLELIC: "gnomad_biallelic.vcf.gz"
RG: ""
INTERVALS: "intervals.list"
PON_DB: "pon_db" #PON_DB path
THREADS: 4
AFONLYGNOMAD: af-only-gnomad.hg38.vcf.gz
NORMALS_PANEL: "pon.vcf.gz"
MEMORY: "-Xmx40g"