ReMM score question

[drseb]

Hi,

not sure this is the right repo. I am happy to open this issue anywhere else, if needed.

In the ReMM-file ReMM.v0.3.1.tsv.gz, I cannot find a score for the position 14:7180825-7180827C>A.

Can you help me debug this? Is this a valid position? If yes, why is it not in ReMM? If no, why not?

[visze]

Hi,

thx for your question. All 3 positions have an ambiguous position (N). So you cannot have a variant C>A here.

samtools faidx GRCh37.p13.genome.fa chr14:7180825-7180827
>chr14:7180825-7180827
NNN

The ReMM score is only precomputed for all unambiguous (i.e., not ‘‘N’’) positions of the human reference genome (release hg19). See

Smedley, Damian, et al. 
"A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease." 
The American Journal of Human Genetics 99.3 (2016): 595-606.