Mappability file for hg38

[katherinef]

Hello,

Is it possible to provide the mappability file for hg38? I'm sure it's something a lot of people will require for use with CLAMMS.

Best wishes

Kath

[katherinef]

I have tried lifting over the hg19 75mer mappability file to hg38 coordinates using the liftOver tool. There are something like ~38,000 regions that are unlifted. Is this sufficient as a fix for running CLAMMS on hg38 data?

[katherinef]

SOLUTION: I've made the mappability file myself using the static version of GEMTools (https://gemtools.github.io/). I used the following commands (where -t/-T options give number of threads) to produce the mappability file and then convert to wig:

gemtools index -i genome.fa -o genome.gem -t 20
gem-mappability -I genome.gem -l 75 -o genome_75mer -T 20
gem-2-wig -I genome.gem -i genome_75mer.mappability -o genome_75mer