config.yaml

all:
    REF: /net/nfs/PAT/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa
    THREADS: 8
    Java_mem: -Xmx4g
    HG19_DICT: /net/nfs/PAT/data/ref/hg19/hg19.dict
    targets: /net/nfs/PAT/home/matias/data/manifests/BCNHL_Seq_v3/BCNHLv3_primary_coord.bed
    genome_build: GRCh37.75
    dbsnp: /net/nfs/PAT/home/matias/dbSNP/b151/All_20180423.vcf.gz
    clinvar: /net/nfs/PAT/home/matias/dbSNP/b151/clinvar_20180701.vcf.gz
    Cosmic: /net/nfs/PAT/home/matias/data/ref/cosmic/hg19_v84_2018/CosmicCodingMuts_BCNHLv3_v84_hg19.vcf
    gnomAD: /net/nfs/PAT/home/tjitske/dbSNP/gnomAD/2.0.2/retagged_gnomad.exomes.r2.0.2-AF.vcf.gz
    HMF_PON: /net/nfs/PAT/home/matias/data/blacklist/HMF_PON/PON.vcf.gz

VarScan_snps:
    min_cov: 5
    min_reads2: 2
    min_avg_qual: 20
    min_var_freq: 0.01
    p_value: 0.05
    strand_filter: 0
    output_vcf: 1
    variants: 0

VarScan_indels:
    min_cov: 5
    min_reads2: 2
    min_avg_qual: 20
    min_var_freq: 0.01
    p_value: 0.05
    strand_filter: 0
    output_vcf: 1
    variants: 0

LoFreq:
    min_cov: 10
    min_mq: 20
    min_bq: 20
    min_alt_bq: 20
    max_depth: 1000
    sig: 0.05

VarScan_Filter:
    #SnpSift_filter: "(GEN[0].SDP>8) & (GEN[0].AD>3) & (GEN[0].FREQ>4.99) & (GEN[0].PVAL<0.05) & (GEN[0].ADF>0) & (GEN[0].ADR>0)"
    BED_blacklist: /net/nfs/PAT/home/matias/data/blacklist/PON_VarScan_N24_min2POS.bed
    Gene_blacklist: /net/nfs/PAT/home/matias/data/blacklist/hypervariable_gene_blacklist.bed

LoFreq_Filter:
    af_min: 0.05
    cov_min: 15
    sb_alpha: 0.05
    #SnpSift_filter: "(DP4[2]>2) & (DP4[3]>2) & ((na HRUN) | (HRUN<8))"
    BED_blacklist: /net/nfs/PAT/home/matias/data/blacklist/PON_LoFreq_N24_min2POS_bq20.bed
    Gene_blacklist: /net/nfs/PAT/home/matias/data/blacklist/hypervariable_gene_blacklist.bed