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
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
-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).