SQUID

Usage: squid [options] -b <Input_BAM> -o <Output_Prefix>
Options:
    --help
    --version
    Extra input options:
    --bwa   If input BAM is generated by BWA or SpeedSeq aligner (default assuming STAR aligner)
    -c  string  Chimeric BAM alignment (Required if using STAR aligner)
    -f  string  Genome FASTA file
    Parsing alignment options:
    -pt bool    Phred type: 0 for Phred33, 1 for Phred64 (0)
    -pl int Maximum Length of low Phred score to filter alignment (10)
    -pm int Low Phred score threshold (4)
    -mq int Mapping quality to filter alignment (1)
    Constructing graph options:
    -dp int Maximum distance of aligning positions for concordant alignment (50000)
    -di int Maximum distance of segment indexes for concordant alignment (20)
    -w  int Minimum edge weight (5)
    -r  double  Discordant edge ratio multiplier / normal tumor cell ratio (8)
    -a  int Max allowed degree (5)
    Output options:
    -G  bool    Output gragh file (0)
    -CO bool    Output ordering of connected components (0)
    -TO bool    Output ordering of all segments (0)
    -RG bool    Output rearranged genome sequence (0)
separate chimeric alignment BAM file is required if using STAR aligner.