Question: what is the lowest coverage the human genome can be sequenced at to provide roughly the same resolution as SNP6?
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gravatar for senowinski
20 months ago by
senowinski30
European Union
senowinski30 wrote:

What depth of coverage of the human genome would roughly provide the same copy number resolution of SNP6?

I want to know this so that I can calculate some kind of a b-allele-frequency at roughly the same frequency as SNP6? Where let's say there is a probe every ~0.00189Mb, would this mean a minimum depth of coverage of 2x? If there are gains and losses this would mean the allele frequency could then be calculated from bps where there are 4 reads mapped?

Thoughts please!

Thanks

sequencing snp next-gen • 527 views
ADD COMMENTlink modified 20 months ago by Brian Bushnell16k • written 20 months ago by senowinski30
0
gravatar for Brian Bushnell
20 months ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

2x sounds reasonable to me. To get an exact number, you should run a simulation at various levels of coverage and see what kind of sensitivity you get.

ADD COMMENTlink written 20 months ago by Brian Bushnell16k
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