NGSadmix genotype matrices include a header line and two beginning columns (with headers) with the marker ID (scaffold and position) and the reference and alternative allele (all sites must be biallelic). Three genotype likelihoods are given for each sample and marker in a standardized format (sum to 1.0) and correspond to the likelihood of increasingless less reference alleles (homozygous reference, heterozygous, homozygous alternative). All values are space-delimited and missing data is coded as 0.000 across all three allele combinations. Here is an example with three samples at two markers:
Marker Ref. Alt. Sample1 Sample1 Sample1 Sample2 Sample2 Sample2 Sample3 Sample3 Sample3
scaffold1_100 A C 1.000 0.000 0.000 0.333 0.333 0.333 0.250 0.750 0.000
scaffold2_1000 G T 0.000 0.000 0.000 0.500 0.500 0.000 0.010 0.990 0.000
The following RADpipe command will create this as output from a filtered VCF:
python genotypes_from_VCF.py --samplesheet <samplesheet.txt> --fi