config.yaml

SAMPLES: "samples.tsv" 
PAIRED: TRUE 
GENOME: "Homo_sapiens_assembly38"
DBSNP: "Homo_sapiens_assembly38.dbsnp138.vcf"
INDELS: "Homo_sapiens_assembly38.known_indels.vcf.gz"
GOLD_STANDARD: "Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
Axiom_Exome: "Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz"
G_phase1: "1000G_phase1.snps.high_confidence.hg38.vcf.gz"
G_omni2: "1000G_omni2.5.hg38.vcf.gz"
hapmap_3: "hapmap_3.3.hg38.vcf.gz"

PL: "Illumina"
ALL_VCF: "WES"
ANNOVAR: /mnt/data/annovar
humanDB: /mnt/data/annovar/humandb
annovar_prefix: "hg38_multianno"
version : hg38

INTERVALS_FILE : 'intervals.list'
GENOMEDB: "my_database"
THREADS: 2


#General filtering parameters 
QD: 2.0 
QUAL: 30.0 
ExcessHet:  54.69

#SNPs filtering Parameters 
SNP_SOR: 3.0 
SNP_FS: 60.0 
SNP_MQ: 40.0 
SNP_MQRankSum: -12.5 
SNP_ReadPosRankSum: -8.0 

#INDELs filtering parameters 
INDEL_FS: 200
INDEL_ReadPosRankSum: -20.0