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Recently got a project on human data. It is easy to find out all the mutations. But how do I exclude all the know Polymorphisms, any approach? Thanks!
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A common approach is to annotate your results with the information from dbSNP, 1000 Genomes, Exome Variant Server .
These databases have information on previously described SNPs and their frequency in several populations.
You can download these databases and annotate your vcf files with them using snpSift annotate.
cheers,
Sophia -
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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