pgsc_calc

pgsc_calc copied to clipboard

Tasks: - [x] Handle other panels/population labels in the report (colour schemes) (closed by https://github.com/PGScatalog/pgsc_calc/commit/c4719f49f85c25dc6a7ced496ebe22fa8be81ec1) - [ ] OCE is missing from the current version of the reference panel (not...

smlmbrt

### Description of feature It's confusing that the other inputs for score download are `pgs_id` and `pgp_id` but the traits are called `trait_efo`. Suggest we change this to `efo_id` or...

smlmbrt

Check sampleset ID doesn't include and underscore (_)

1

https://github.com/PGScatalog/pgsc_calc/blob/8bdf287d558a7abe1ef86e961337df71d7289d0d/lib/SamplesheetParser.groovy#L175-L182 This module needs to check for reserved names as was done in the old sample sheet checking (no 'reference' or '_'): https://github.com/PGScatalog/pgscatalog_utils/blob/6da7eb0e157ba4e73f941233ee8d8ae4fb5e3926/pgscatalog_utils/samplesheet/check.py#L306-L322

smlmbrt

The variants are undermatched.

1

I used the following code to calculate PGS for my UK biobank research by PGS003765 research results, and successfully obtained the result, but my variants matched only 12.9%. Is this...

Linlin1213a

run_ancestry failed on test data

3

### Description of the bug Maybe similar to https://github.com/PGScatalog/pgsc_calc/issues/252, but haven't found a resolution yet. - initial step without ancestry adjustment, `nextflow run pgscatalog/pgsc_calc -profile test,docker` completes successfully. - running...

ashenfernando1

Improvements to PCA steps & default reference panel

1

## Ideas for making PCA projections more robust - [ ] Subsetting to a smaller set of PCA eligible variants? - HapMap3 (same as `bigsnpr`) - Ancestry informative markers (similar...

smlmbrt

Update plink version?

2

Might be worthwhile updating to a newer version of plink? Some bug-fixes might be useful: - Alpha 4 has faster LD-pruning - Read freq improvements https://github.com/chrchang/plink-ng/releases/tag/v2.00a4.2

smlmbrt

I switched to singularity with your modification and was able to get past the sorting issue. After rerunning, I was receiving this error with FRAPOSA: ``` Jan-29 13:08:17.508 [Task monitor]...

smlmbrt

### Description of feature https://github.com/PGScatalog/pgsc_calc/discussions/117 Digging through `work/` is confusing and bad UX!

nebfield

Reference creation: current docs/code doesn't support other data

1

### Description of the bug Tried to follow instructions (https://pgsc-calc.readthedocs.io/en/latest/how-to/database.html#optional-create-reference-database) but had to edit code to get the bootstrap to run on a new dataset. The channels still get messed...

smlmbrt