Jules Jacobsen

This is related to/partly duplicates #265

@pnrobinson If you're running an branch other than master, this is possible. Which branch did this occur on?

The data is in the JSON output file. If you need TSV you can use something like [jq](https://stedolan.github.io/jq/manual/) to slice the JSON output into TSV if you like. TSV isn't...

Have you added the REMM and CADD scores to the `pathogenicitySources: `? Note also that REMM is trained on non-coding variants so if you're analysing exome data you'll not see...

The gene/disease phenotype matches are available in the JSON output. Please use that if you need it.

@oleraj @PabloBotas and @damiansm would you want to be able to define this manually, or expect the system to do this as a default? I'm guessing the latter as not...

@oleraj yes, that was what I was asking. The problem is how to define that you do or don't want to use it? If it's a non-user-alterable default, then this...

You should adapt the `examples/test-analysis-exome.yml` file and run that using the `--analysis` option. The commands you're trying to run are from versions

Certainly worth looking into - will want to wait for the new Ensembl build as they will update their gnomAD data to the latest version ad we're using their combined...

Exomiser data hg19_2007 source | rs141509078 | rs146768859 -------|---------------|----------- THOUSAND_GENOMES | 0.13980001 | 0.13980001 TOPMED | 0.077250004 | 0.05415 ESP_EUROPEAN_AMERICAN | - | 0.0116 ESP_ALL | - | 0.0077 EXAC_AMERICAN...