modules/quilt_quilt
QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.
Description
QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel.
Input
(Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab separated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized.
*.{txt}
(Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab separated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header.
*.{txt}
(Optional) Path to gen file with high coverage results. Empty for no genfile. If both genfile and phasefile are given, only phasefile is used, as genfile (unphased genotypes) is derivative to phasefile (phased genotypes). File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = hom ref, 1 = het, 2 = hom alt and NA indicating missing genotype, with rows corresponding to rows of the posfile. Note therefore this file has one more row than posfile which has no header [default ""]
*.{txt}