config.yaml

samples: list.txt
adapters:
    SE: "adapters_SE.fa"
flexbar:
    adapter-trim-end: "RIGHT"
    adapter-min-overlap: 7
    pre-trim-left: 5
    max-uncalled: 150
    min-read-length: 25
    qtrim: "TAIL"
    qtrim-format: "sanger"
    qtrim-threshold: 20
    zip-output: "GZ"
bt2idx: "refs/hg19/Sequence/Bowtie2Index/genome"
bowtie2:
    sensitive: ""
    rg: "PL:IonTorrent"
mh_bedfile: "refs/chr1_mh.bed"
fasta_ref: "refs/hg19/Sequence/Bowtie2Index/genome.fa"
freebayes:
    variant:
        min-alternate-count: "5"
        min-mapping-quality: "20"
        min-base-quality: "30"
        use-duplicate-reads: ""
    haps:
        min-mapping-quality: "20"
        min-base-quality: "30"
        use-duplicate-reads: ""
        min-repeat-size: "0"
        no-partial-observations: ""
        max-complex-gap: "400"
        haplotype-length: "500"
vcffilter_qual: 20