Computational protocol: Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

Similar protocols

Protocol publication

[…] Whole blood samples were collected from 277 extended families (546 nuclear families, 1484 persons). Subsequently, DNA was extracted from these samples, and genetic variations of single nucleotide polymorphisms (SNPs) at 26 genetic loci were characterized for each individual. The results obtained 172k-byte pedigree data file for following analysis. For the FBAT program, the original Linux executable was installed on the cluster. The hbat -e interactive command of FBAT was used for ConsWH and CombWH analysis, and the -e option was implemented to account for the bias introduced by studying multiple members from the same family. For the Unphased program, its version 3.0.10 source code was recompiled with the GNU C compiler with the option -march = pentium4 -O2 for the CPU-specific optimization. Unphased was used with -uncertain and -certain options from the command-line instead of its graphical user interface written in Java. The former option includes ambiguous genetic data to increase the sensitivity, whereas the later option evaluates only known genetic data, resulting in much quicker analysis. […]

Pipeline specifications

Software tools FBAT, UNPHASED
Application GWAS
Organisms Homo sapiens