The 'samtools mpileup' command was used to generate genotype likelihoods (GLs) at all MAC2 sites on a per sample basis from each sample’s BAM file. The pipeline and software versions have been made available online (see URLs). The resulting BCF files were merged using the 'bcftools merge' command and the MAC2 sites and alleles extracted using the 'bcftools call' command. The use of 'bcftools call' here made a baseline set of non-LD based genotype calls for each site across all samples. These calls were used for some initial sample QC (see Sample filtering section). We calculated GLs on 33,070 samples in total.
