Variant reports are not the right deliverable for a re-sequencing study.
A well written technical blog ‘MassGenomics‘ written by Dan Koboldt illustrates why. Dan says “What’s more, with the advent of next-generation sequencing, I hate to tell you, but people are going to be reporting a lot of false positives. I guarantee it. So when you filter all of the variants, you might actually remove the ones you’re looking for.”
Its easy to see why researchers are not enthusiastic about tabular reports. They want to get into the data on their own, without intermediaries, and they want software to facilitate that, not be in the way.
