search

mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
144 stars 67 forks source link

Different read depth of sequencing. #122

Open huangyizR opened 5 years ago

huangyizR commented 5 years ago

Hi, Just wondering if I have multiple WGS data with different reads depth, do I need to standardized the reads depth by normal tissue?

Best, Peter

veseshan commented 5 years ago

FACETS analyzes single tumor-normal pair at a time. The log-ratio is a (local) ratio of tumor to normal depth. So standardization is built-in. But if you mean, should the library size of the normals be the same across different pairs, then no you don't.

kobejamescurry commented 5 years ago

@veseshan is it convinient for you to have a look at my issues, thanks a lot. I am really need your help

another one issue, can you clarify why the log OR is a symmetrical aixs, for a given loci, the log OR should be a certain value, why there has two , thanks a lot

veseshan commented 5 years ago

@kobejamescurry - You need to find another way of learning about genetics and assay technologies such as micro-array or sequencing rather than posting them as issues. This way you can understand concepts such as whether a snp in the population need to be heterozygous in a subject, phasing (which allele comes from which parental chromosome), assay's ability ability to detect polymorphism, sequencing depth etc.