Output
squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)
*.geno.ld
test for genotype independence via the chi-squared statistic (optional)
*.geno.chisq
r2 statistics of the sites contained in the provided input file verses all other sites (optional)
*.list.hap.ld
r2 statistics of the sites contained in the provided input file verses all other sites (optional)
*.list.geno.ld
r2 statistics for sites (haplotypes) on different chromosomes (optional)
*.interchrom.hap.ld
r2 statistics for sites (genotypes) on different chromosomes (optional)
*.interchrom.geno.ld
Transition / Transversion ratio as a function of alternative allele count (optional)
*.TsTv.count
Transition / Transversion ratio as a function of SNP quality threshold (optional)
*.TsTv.qual
Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)
*.FILTER.summary
Nucleotide diversity in windows, with window size determined by options (optional)
*windowed.pi
Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)
*.hwe
Tajima’s D statistic in bins with size of the specified number in options (optional)
*.Tajima.D
Number of variants within each individual of a specific frequency in options (optional)
*.ifreqburden
Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)
*.relatedness
Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)
*.relatedness2
Histogram file of the length of all indels (including SNPs) (optional)
*.indel_hist
Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)
*.FORMAT
Genotypes output as large matrix.
Genotypes of each individual on a separate line.
Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.
Missing genotypes are represented by -1 (optional)
*.012
Details the individuals included in the main genotypes_matrix file (optional)
*.012.indv
Details the site locations included in the main genotypes_matrix file (optional)
*.012.pos
Sites that are common / unique to each file specified in optional inputs (optional)
*.diff.sites.in.files
Individuals that are common / unique to each file specified in optional inputs (optional)
*.diff.indv.in.files
Discordance on a site by site basis, specified in optional inputs (optional)
*.diff.sites
Discordance on a individual by individual basis, specified in optional inputs (optional)
*.diff.indv
Discordance matrix between files specified in optional inputs (optional)
*.diff.discordance.matrix