how to run FATHMM-MKL program based on hg38?

Question

[kamanovae]

Hi! I am trying to annotate vcd file using FATHMM-MLK program (https://github.com/HAShihab/fathmm-MKL). There is only hg19 database in the githab repository. I found a database based on hg38 for these purposes, but the result shows that it doesn’t fit or I’m doing something wrong. (https://zenodo.org/record/3981121#.YFQ9Wi9c41I)

now my results look like this:

1 916549 A G No Prediction Found

1 935222 C A No Prediction Found

1 11854785 C T No Prediction Found

1 11854786 C T No Prediction Found

can someone tell me what I'm doing wrong?

Answer 1

[Kevin Blighe]

Best thing to do is contact the authors in Bristol, UK. They likely have a GRCh38 dataset available. Otherwise, you will have to 'lift over' the hg19 / GRCh37 co-ordinates via the command line. There are ways to do this, accessible via a search.

Kevin