Gabe points out in great detail a bug he found in GATK's variant caller which has be widely regarded as a reliable SNP caller.
I think in general the 'unreliable' nature of next gen seq data has researchers often seeking multiple sources of confirmation for variants before moving to publication.
though I am frankly surprised that GATK turned up an error but as Gabe points out it might be common to find Heisen Bugs in software.
and it's a poignant reminder that DTC genetic testing needs more work to avoid mistakes like these that might be detrimental to personalised medicine
"But my scary homozygous insertion (row 2) shows 153 reference bases and no reads supporting the insertion. Yet it was still called a homozygous variant!