LiterallyUniqueLogin

Writing new values for FILTER field

2

Hi there, I'd like to be able to write new values to the filter field as part of writing out a new VCF. But I get the following issue: ```...

We need testing around ploidy

1

Which tools can handle haploid data? (GangSTR is one) Are any of these tools not human specific and can handle ploidy >2? For those cases we should add test cases...

REPCN is currently specified as ``` ##FORMAT= ``` but the number isn't 2 - it's the ploidy of the sample, e.g. 2 for all autosomes and 1 for male non-psuedoautosomal...

Add home to source paths

3

#### For bugs - Rule Id (if any, e.g. SC1090): - My shellcheck version (`shellcheck --version` or "online"): 0.7.0 - [X] The rule's wiki page does not already cover this...

Cromwell should issue warnings when it encounters config it doesn't recognize

2

I had `hasing-strategy` instead of `hashing-strategy` in my config and lost loads of hours trying to debug the unbearably slow caching I was experiencing, and it turns out that the...

dxCompiler possibly incorrect localizes input file expressions

11

I'm compiling the following WDL ``` task load_shared_covars { input { String script_dir File script = "~{script_dir}/traits/load_shared_covars.py" File python_array_utils = "~{script_dir}/traits/python_array_utils.py" } output { ... } command > runtime {...