Saw figure 2 from this paper from Stephan Schuster in talks wayyy back and his point about using different platforms/chemistry to reduce bias was always in the back of my head when handling single platform data.
Great work getting this finally published.
His criteria for variant calling should be also a good starting reference point.
"We used SAMtools version 0.1.16 to call the variants in the Illumina reads. We required a minimum coverage of 4, a maximum coverage of 60 and a minimum quality of 20 for the SNPs and indels that were found to be on the autosomes. We reduced the maximum coverage requirement to 45 for the sex chromosomes and increased it to 10,000 for the mitochondrial DNA. Only homozygous SNP and indels calls were kept from the sex chromosomes and mtDNA."