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config.yaml
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#########################
## SNAKEFILE SAMPLES ##
#########################
samples:
ERR696683_chr3: data/original_bam/filtering/ERR696683_chr3.bam
ERR753368_chr3: data/original_bam/filtering/ERR753368_chr3.bam
ERR753369_chr3: data/original_bam/filtering/ERR753369_chr3.bam
ERR753370_chr3: data/original_bam/filtering/ERR753370_chr3.bam
ERR753371_chr3: data/original_bam/filtering/ERR753371_chr3.bam
ERR753372_chr3: data/original_bam/filtering/ERR753372_chr3.bam
ERR753373_chr3: data/original_bam/filtering/ERR753373_chr3.bam
ERR753374_chr3: data/original_bam/filtering/ERR753374_chr3.bam
ERR753375_chr3: data/original_bam/filtering/ERR753375_chr3.bam
ERR753376_chr3: data/original_bam/filtering/ERR753376_chr3.bam
ERR753377_chr3: data/original_bam/filtering/ERR753377_chr3.bam
ERR753378_chr3: data/original_bam/filtering/ERR753378_chr3.bam
########################
## SNAKEFILE PARAMS ##
########################
samples_names:
ERR696683_chr3
ERR753368_chr3
ERR753369_chr3
ERR753370_chr3
ERR753371_chr3
ERR753372_chr3
ERR753373_chr3
ERR753374_chr3
ERR753375_chr3
ERR753376_chr3
ERR753377_chr3
ERR753378_chr3
## Choose your chromosome
chromosome: chr3
# Chromosome 3, 5, 7, 12, 17 ENSEMBL:
# https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.3.fa.gz
# https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.5.fa.gz
# https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.7.fa.gz
# https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.12.fa.gz
# https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz
url_reference_genome: https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.3.fa.gz
## Fixing the fastq files, FASTP parameters:
fastp_cuttail: 30
fastp_cutfront: 30
fastp_cutmeanq: 30
fastp_length: 75
## Extracting variants
ref_genome_name_file: genome.fa
# Min reads that has to be mapping to considerate a variant
min_reads_variant: 5
## Doing VEP for variant annotation
vep_species: homo_sapiens
vep_assembly: GRCh38
## Gene That you want to filter in the VCF using R
## PIK3CA (chromosome 3); APC (chromosome 5); BRAF (chromosome 7); KRAS (chromosome 12) ;TP53 (chromosome 17)
gene_to_filterR: PIK3CA