PASS or all variants from ExAC for allele frequencies?

jeremymcrae / recessiveStats

repository for analysis of recessive genes

GNU General Public License v2.0

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PASS or all variants from ExAC for allele frequencies? #3

Open monkollek opened 8 years ago

monkollek commented 8 years ago

Wondering if you are using site filters? As letting in too many bad indels will inflate the frameshift/lof frequencies

jeremymcrae commented 8 years ago

Hmm, yes. I have included all variants, regardless of their quality metrics. Do you have an idea about how much this would bias the frequency on average?