translocation-snake/config.yaml at master · tgac-vumc/translocation-snake · GitHub

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ALL:
    THREADS: 4
    REF_CHR: /net/nfs/PAT/home/tjitske/files/ref/incl_chr/hg19.fa
    REF_NOCHR: /net/nfs/PAT/home/tjitske/files/ref/excl_chr/hg19_refgen_exclchr.fa
    Annotationfile: code/annotation_new_BCNHL-v2.bed
    targets: code/BCNHLv2_primary_coord.bed

filters:
    splitread: 4         #number of mininimal amount of split read evidence
    discread: 3          #number of minimal amount of discordant read evidence
    novoscore: 4         #minimal novobreak QUAL score
    gridssscore: 450     #minimal gridss QUAL score
    highSVevidence: 7   #minimal amount of split reads and discordant reads required for structural variants to be called High evidence
    blacklist: code/180307-blacklist.bed         #blacklist in bedfile format

gridss:
    GRIDSS_JAR: /net/nfs/PAT/home/tjitske/GRIDSS/gridss-1.4.2-jar-with-dependencies.jar

wham:
    WHAM: /net/nfs/PAT/home/tjitske/WHAM/wham/bin/wham
    CLASSIFY: /net/nfs/PAT/home/tjitske/WHAM/wham/utils/classify_WHAM_vcf.py
    TRAIN: /net/nfs/PAT/home/tjitske/WHAM/wham/data/WHAM_training_data.txt
    MAPQUAL: 10
    BASEQUAL: 5

novobreak:
    NOVOBREAK: /net/nfs/PAT/home/tjitske/novobreak/nb_distribution/run_novoBreak.sh
    EXE_DIR: /net/nfs/PAT/home/tjitske/novobreak/nb_distribution
    NORMAL: /net/nfs/PAT/analysis/MPS-310/Blood_combined_bam/combined_healthy_blood_nochr.bam
    HEADER: /net/nfs/PAT/home/tjitske/novobreak/nb_distribution/header.txt

breakmer:
    BREAKMER: /net/nfs/PAT/home/tjitske/BreaKmer/new_2016-05-26/BreaKmer-master/breakmer.py
    targets_bed_file: code/BCNHL_Seq_V2_allTRL.bed
    analysis_name: _BCNHL_Seq_V2_allTRL
    reference_data_dir: /net/nfs/PAT/home/tjitske/BreaKmer/new_2016-05-26/BreaKmer-master/reference
    cutadapt_config_file: /net/nfs/PAT/home/tjitske/BreaKmer/new_2016-05-26/BreaKmer-master/cutadapt.cfg
    cutadapt: /net/nfs/PAT/lib/cutadapt/cutadapt-1.1/bin/cutadapt
    jellyfish: /net/nfs/PAT/home/tjitske/Jellyfish/jellyfish-2.2.6/bin/jellyfish
    gene_annotation_file: /net/nfs/PAT/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/refGene.txt
    kmer_size: 15