kcoeff

kcoeff usage

The input format is a tab-delimited file. The header row consists of chromosome, position, individual identifiers (IID). The following rows include chromosome, position, and genotypes with the following format:

AA corresponds to 0
AB corresponds to 1
BB corresponds to 2
No call corresponds to -1

A sample file (sample_file.txt) is included with the corresponding pedigree (pedigree.ppt)(see Sample Data section).

USAGE:
cat sample_file.txt | ./kcoeff -win_size 400 -threads * > results.txt

Please note that the window size is variable. We recommend a window size of at least 300 and note that window sizes greater than 600 will reduce accurate estimates of IBD0, 1, and 2. * denotes an option for users with multiple cores. The default is set to 1. An average of 50 comparisons are performed per minute per core based on an average of 900,000 SNPs. There is no limit to the number of SNPs; however, increasing SNP number increases program time linearly. This program only works autosomal SNPs.