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CLI: view

Synopsis

Convert binary TWO->LD/TWO, subset and slice TWO data

Examples

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tomahawk view -i 1kgp3_chr20.two -I 20:10e6-11e6 -u -r 0.3 -R 0.5
tomahawk view -i 1kgp3_chr20.two -I 20:10e6-11e6,20:10e6-11e6 -r 0.3
tomahawk view -i 1kgp3_chr20.two -I 20:10e6-11e6,20:20e6-21e6 -I 20:10e3-100e3 -u -p 1e-6

Options

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Options:
  -i FILE   input TWO file (required)
  -h/H      (twk/two) header only / no header
  -I STRING filter interval <contig>:pos-pos (TWK/TWO) or linked interval <contig>:pos-pos,<contig>:pos-pos
  -o FILE    output file (- for stdout; default: -)
  -O <b|u>   b: compressed TWO, u: uncompressed LD

Filter parameters:
  -r,-R --minR2,--maxR2   FLOAT   Pearson's R-squared min/max cut-off value
  -z,-Z --minR,--maxR     FLOAT   Pearson's R min/max cut-off value
  -p,-P --minP,--maxP     FLOAT   Min/max P-value (default: [0,1])
  -d,-D --minD,--maxD     FLOAT   Min/max D value (default: [-1,1])
  -b,-B --minDP,--maxDP   FLOAT   Min/max D' value (default: [0,1])
  -1,-5 --minP1,--maxP1   FLOAT   Min/max REF_REF count (default: [0,inf])
  -2,-6 --minP2,--maxP2   FLOAT   Min/max REF_ALT count (default: [0,inf])
  -3,-7 --minQ1,--maxQ1   FLOAT   Min/max ALT_REF count (default: [0,inf])
  -4,-8 --minQ2,--maxQ1   FLOAT   Min/max ALT_ALT count (default: [0,inf])
  -a,-A --minMHC,--maxMHC FLOAT   Min/max number of non-major haplotype count (default: [0,inf])
  -x,-X --minChi,--maxChi FLOAT   Min/max Chi-squared CV of contingency table (default: [0,inf])
  -m,-M --minMCV,--maxMCV FLOAT   Min/max Chi-squared CV of unphased model (default: [0,inf])
  -f  INT  include FLAG value
  -F  INT  exclude FLAG value
  -u       output only the upper triangular values
  -l       output only the lower triangular values