Originally posted by nilshomer
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Hi, Nils.
I was perusing their website and wasn't sure if I was at the right place, but it was the analysis page. Looking there, I understand they use multiple SNP callers to get the overlap and this reduces up to 30% of false positives for low with coverage? Would you say in your own opinion that it's vital to have two different assemblies from different programs when comparing the SNP calls or would two separate SNP callers on one alignment dataset be, well, good? It's necessary I make these calls in the quickest amount of time.
I need to align my reads in a much quicker method as BioScope has a very poor runtime, but I do appreciate BioScope's high fidelity in percentage of mapped reads. What additional percentage of mapping would you expect with BFAST? I think outside of BioScope, your's is the best open-source alternative. As far as runs are concerned, I find it very difficult to gauge a run outside of error rate. Do you have any recommendations for gauging run quality other than heat maps and cycle scans? It seems there are so many variable factors that go into the prep that two runs may appear good quality and yet it doesn't map over > 80 % with the same parameters as a similar run. I'd love to hear your thoughts on all these topics, as you have much experience? Thank you.
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