The pipeline only outputs variant sites for each sample
Since a commit last year, the pipeline only outputs variant sites for each sample: 1bcdc343
This is not wrong in itself, since all variants are available from the g.vcf file. However, this leads to unfortunate interactions when comparing VCF files to array files, since after this change there are no more homref sites in the sample VCF files. This reduces the sensitivity of any subsequent array checks.