Open AlistairNWard opened 6 years ago
Currently, we have variants displayed in a fold frequency fashion along the y-axis. We'd like to incorporate some more statistically rigorous metric to this display, or perhaps in a filter.
Thinking simple Fisher's Exact Test would be appropriate. Would this be a filter, an alternate main view, a view within the popup... etc?
Toggle with manhattan plot style
The default should probably be the Manhattan plot based on this test. This is a view people are familiar with
Suggestions from H. Coon & N. Camp:
Suggestions from G. Marth & A. Farrell at lab meeting 08/28:
Quality might be not that useful, but other values would be good.
Allele count / allele frequency / allele balance We want to have a minimum coverage for the locus (say 20x, but we can play around with these). If a het, we would expect to see ~50% alt allele. So maybe demand at least 25% alternate allele frequency.
We also expect there to be observations from forward and reverse strand, so make sure we see representation of the alt allele from both strands.
How is enrichment being calculated?
It would be good to see raw information on the how many samples harbour each variant. If there are n=N probands and n=M in the subset, it would be good to see that x of N, and y of M samples harbour the variant. This would show in the summary panel when you select the variant, and the y position showing enrichment would help the user which variants to look closer at.
Longer term, we should think how we can get additional information, e.g. the number of de novos or different zygosities.