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CLI: calc

Synopsis

Calculate linkage disequilibrium from pairs of SNVs. Force phased -p or unphased -u for faster calculations if all variant sites are guaranteed to have the given phasing.

Examples

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tomahawk calc -i in.twk -o output.two -t 28
tomahawk calc -pi in.twk -c 45 -C 1 -t 28 -r 0.2
tomahawk calc -ui in.twk -w 4000000 -t 28 -r 0.3 -k 10

Options

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Options:
  -i FILE   input Tomahawk (required)
  -o FILE   output file or file prefix (required)
  -t INT    number of CPU threads (default: maximum available)
  -c INT    number of subproblems to split compute into (must be in (c!2 + c))
  -C INT    chosen part to compute (0 < -C < -c)
  -m        run in low-memory mode: this is considerably slower but use no more memory than
               block1*variants + block2*variants
  -M        use phased bitmaps in low-memory mode. Automatically triggers -m and -p.
  -b        number of records in a block. Has an effect on memory usage only when -m is set.
  -w INT    sliding window width in bases
  -I STRING filter interval <contig>:pos-pos (see manual)
  -p        force computations to use phased math
  -u        force computations to use unphased math
  -P FLOAT  Fisher's exact test / Chi-squared cutoff P-value (default: 1)
  -r FLOAT  Pearson's R-squared minimum cut-off value (default: 0.1)
  -k INT    compression level to use (default: 1, max = 22).