<p>I came across a lot of literature that uses 30x reads as a good coverage depth for NGS. But then I read up on Broad's NGS intro where they used "high-pass: 30x; low-pass: 4x; exon capture:150x". Not sure when the intro note was written, so no idea how relevant those numbers are to HiSeq 2000 machine.</p>

<p>Q1. how do they come up with those numbers? (anything to do with their Bayesian model-based SNP calling ?)</p>

<p>Q2. how are those numbers related to detecting rare SNPs in a small pool of sample? Say, I want to find out a SNP whose population-based occurrence is between 0.1-0.01%. I only have a handful of individual samples (say 20). Should I adjust the coverage depth (say, from 30x to 100x) in order to detect with high confidence the SNP of interest?</p>

<p>Some digging around in google and pubmed does not really help me find the answers. Any help/reference will be greatly appreciated. Thank you. </p>

<p>This is a hard question to answer definitively. It really depends on what you are trying to do and especially what kind of samples you are profiling. What is the expected purity of your sample?  Is there contamination or heterogeneity expected?  If the answer to those last two questions is yes, then you will want more coverage to detect variants at lower frequency due to impurity or because they come from minor (but possibly still interesting) subpopulations of your sample.  We tend to target 200-250x for tumor studies for the reasons described above. But, I don't think there is a really solid statistical basis for that choice. The cost-benefit analysis is probably too complex for a definitive answer so practical considerations such as cost tend to take greater precedence. </p>

<p>If you are looking for a very rare SNP in a population of individuals (rather than a population of cells in a single sample) then I don't think extra coverage is nearly as important as sampling more individuals. If a SNP is only found in 0.01% of the population then it is highly unlikely that you will detect it in a sample of 20 individuals no matter how deeply you sequence. Chances are the SNP just isn't there. Am I missing something in your question?</p>

<p>Here are other related BioStar questions:</p>

<ul>
<li><a href='/p/12506/'>What depth of coverage for whole genome SNP calling?</a></li>
<li><a href='/p/3703/'>What coverage is required for ChIP-Seq experiments?</a></li>
<li><a href='/p/65501/'>How much coverage do we need for an RNA-seq experiment?</a></li>
</ul>
