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TRGT-denovo command-line options

Command: trio

Basic:

  • -r, --reference <FASTA> Path to the FASTA file containing the reference genome. The same reference genome as was used for read alignment.
  • -b, --bed <BED> Path to the BED file with reference coordinates of tandem repeats
  • -m, --mother <PREFIX> Common (path) prefix of spanning reads BAM file and variant call VCF file of mother
  • -f, --father <PREFIX> Common (path) prefix of spanning reads BAM file and variant call VCF file of father
  • -c, --child <PREFIX> Common (path) prefix of spanning reads BAM file and variant call VCF file of child
  • -o, --out <CSV> Output csv path
  • --trid <TRID> Optionally a tandem repeat ID may be supplied, if so, only this site will be tested, default = None
  • -@ <THREADS> Number of threads, the number of sites that are processed in parallel, default = 1
  • -h, --help Print help
  • -V, --version Print version

Advanced:

  • --flank-len <FLANK_LEN> Number of flanking nucleotides added to a target region during realignment, default = 50
  • --no-clip-aln Score alignments without stripping the flanks
  • --parental-quantile <QUANTILE> Quantile of alignment scores to determine the parental threshold, default is strict and takes only the top scoring alignment, default = 1.0
  • --aln-scoring Scoring function for 2-piece gap affine alignment (non-negative values): mismatch,gap_opening1,gap_extension1,gap_opening2,gap_extension2, default = "8,4,2,24,1", see here for more details on parametrization