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aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
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assume GQ = 20 in the absence of GQ tags within the provided VCF #60

Closed aryarm closed 3 years ago

aryarm commented 3 years ago

add an option to the pipeline for this?

the GQ is used by the allelic imbalance test as a prior that the genotype is incorrect, but GQ = 20 (ie a genotyping error of 0.01) is a reasonably conservative assumption