Ben Weisburd

Thanks, yes. I know it's standard to generate missing genotypes in SNP calling pipelines, when there's no coverage etc. and it's not considered an error. IIUC, EH also doesn't treat...

The difference is often because the precomputed scores were generated by running SpliceAI with a max distance of 50bp, while https://spliceailookup.broadinstitute.org/ has a default of 500bp. . You can check...

If other users would like to see support for dictionaries, please post your views here or in https://github.com/bw2/ConfigArgParse/issues/258

A PR to add this would be appreciated.

If other users have this issue, please post here. My initial sense is that this is a rare / unusual use case.

also the Consequence column

It seems to only occur when I use bp.read_input(..) to localize many files per job. Above a certain number of input files (many thousands), I started getting this error.

Hi Ines, thanks very much for the detailed replies. I've now tried running with `implementation="PCA"` and compared it to `implementation="AE"` which I ran previously. It's significantly faster as expected, but...

Hi @drewjbeh , we have now switched to FRASERv2 (and I've personally moved on to other projects).

The error is actually happening in `plotAberrantPerSample(..)`