Using the sarek pipeline default values. Aligned to HG38 using bwa, and dragmap. Variants are called using either haplotypecaller, strelka, deepvariant, or freebayes. Data input was Agilent 200M WES r
The HELIC study has been whole genome sequencing individuals from 2 Greek isolated populations at 1x depth. The genotype calling process crucially involves a VQSR step followed by imputation-based ref