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TRGT-denovo command-line options

Command: trio and duo

Both the trio and duo commands are used to process tandem repeats, with trio designed for analyzing data from a mother, father, and child, and duo intended for cases with only two individuals. Below are the common and specific options for each command:

Basic Options (Common to both trio and duo):

  • -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
  • -o, --out <TSV> Output tsv 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

Options specific to trio:

  • -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

Options specific to duo:

  • -a, --sample-a <PREFIX> Common (path) prefix of spanning reads BAM file and variant call VCF file of the first sample
  • -b, --sample-b <PREFIX> Common (path) prefix of spanning reads BAM file and variant call VCF file of the second sample

Advanced:

  • --flank-len <FLANK_LEN> Amount of additional flanking sequence that should be used during alignment, default = 50
  • --no-clip-aln Score alignments without stripping the flanks
  • --p-quantile <QUANTILE> Quantile of alignment scores to determine the 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
  • --partition-by-aln Within-sample partitioning using alignment rather than the TRGT BAMleet allele length field.
  • --quick <QUICK> Only test loci that differ by a certain fraction in allele length. Format: , (e.g. AL,0.1 or AL). If no fraction is specified (or fraction is 0), it checks for exact matches. If a fraction is specified, it checks if the relative difference is within the given tolerance.

Verbose Output:

You can increase the verbosity of TRGT-denovo's output by adding a verbose flag before the command:

  • -v Provides verbose output.
  • -vv Provides more detailed verbose output.