Software used

• Cromwell-29 and 31

• Wdltool-0.14

• Plink 1.9 and 2.0

• BCFtools 1.5 and 1.7

• Eagle 2.3.5

• Beagle 4.1 (version 08Jun17.d8b)

• R 3.4.1 (packages: data.table 1.10.4, sm 2.2-5.4)