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CLI: haplotype

Synopsis

Retrieve haplotype strings from individuals in a given range. This is equivalent to slicing out a section of the transpose of the genotype-sample matrix. Outputs a FASTA file or NM-matrix with 2N haplotype strings.

Examples

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tomahawk haplotype -i 1kgp3_chr6.twk -I 6:10e6-10.5e6 -m
tomahawk haplotype -i 1kgp3_chr6.twk -I 6:10e6-10.5e6 -n
tomahawk haplotype -i 1kgp3_chr6.twk -I 6:10e6-10.5e6

Options

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Options:
  -i FILE   input TWK file (required)
  -I STRING interval string for target region
  -m        output haplotypes in tab-delimited matrix form
  -n        output haplotypes [0,1]-encoded instead of FASTA format