Block Output Options

-blockoutput <type>

Generate haplotypes and population frequencies for blocks of <type>, which can be GAB (Gabriel et al), GAM (4 gamete blocks), SPI (solid spine blocks) or ALL (each of the previous 3). The default block type is Gabriel. More information can be found with the blocks help.

-blockCutHighCI <thresh>

Gabriel 'Strong LD' high confidence interval D' cutoff.

-blockCutLowCI <thresh>

Gabriel 'Strong LD' low confidence interval D' cutoff.

-blockMAFThresh <thresh>

Gabriel MAF threshold. Markers below this allele frequency will be skipped in building Gabriel blocks.

-blockRecHighCI <thresh>

Gabriel recombination high confidence interval D' cutoff.

-blockInformFrac <thresh>

Gabriel fraction of informative markers required to be in strong LD.

-block4GamCut <thresh>

4 Gamete block cutoff for frequency of 4th pairwise haplotype.

-blockSpineDP <thresh>

Solid Spine blocks D' cutoff for 'Strong LD'.