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CLI: scalc

Synopsis

Calculate linkage disequilibrium for a single variant versus its neighbourhood.

Examples

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tomahawk scalc -i in.twk -o output.two -t 28 -I 6:10e6-10.1e6
tomahawk scalc -i in.twk -o output.two -t 28 -I 6:10e6-10.1e6 -w 1000000

Options

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Options:
  -i FILE   input Tomahawk (required)
  -o FILE   output file or file prefix (required)
  -I STRING filter interval <contig>:pos-pos (see manual; required)
  -w INT    number of bases to include around the target snp (default: 500kbp)
  -t INT    number of CPU threads (default: maximum available)
  -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.
  -P FLOAT  Fisher's exact test / Chi-squared cutoff P-value (default: 1)
  -r FLOAT  Pearson's R-squared minimum cut-off value (default: 0.0)
  -k INT    compression level to use (default: 1, max = 22).