Pipeline

All the materials were genotyped with the chips according to the manufacturer’s specifications. To obtain high-quality data, we then pruned the data set of discovery stage with the following criteria: sample call rate >99%; SNP call rate >95%; minor allele frequency (MAF) >0.01; and a threshold for Hardy–Weinberg equilibrium of 0.0001 (Fisher’s exact test).

Input files

Under construction.

Output files

Samples’ hapmap format file is output with the pipeline.