I have 4 columns in my annotated VCF "FATHMM_SCORE, FATHMM_PRED, FATHMM_MKL_CODING_SCORE, FATHMM_MKL_CODING_PRED". Can someone please explain what is the difference between these two scores?
I have 4 columns in my annotated VCF "FATHMM_SCORE, FATHMM_PRED, FATHMM_MKL_CODING_SCORE, FATHMM_MKL_CODING_PRED". Can someone please explain what is the difference between these two scores?
FATHMM and FATHMM-MKL are in silico functional prediction tools that were developed by a group at the University of Bristol in England.
FATHMM came first and was tailoured for coding variants - it has 3 sub-algorithms that were built on training datasets of:
When using FATHMM, one should technically choose which sub-algorithm to use.
FATHMM-MKL came later and is tailoured for non-coding variants. It was built on the following data:
[source: https://academic.oup.com/bioinformatics/article/31/10/1536/177080#84558293]
As with all algorithms developed at the time, it was observed that conservation is the single best predictor of pathogenicity.
I list other in silico prediction tools, here: A: pathogenicity predictors of cancer mutations
Kevin
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