pgsc_calc

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* Compares calculated scores to known good scores * Requires about 6.2GB RAM max * Run on publish or through UI (it's a bit slow)

nebfield

smlmbrt

Extra QA for scoring

4

### Description of feature Add additional checks to make sure all variants in the scoring file have been calculated on the samples. Currently this check is only for test data,...

smlmbrt

Allow combined scorefiles as input

1

Either in: - Wide format (e.g. multiple effect_weight columns) - Long format (e.g. a single ID column)

smlmbrt

To ensure the calculator runs when a single-sample is provided, assuming it is from imputed genotype dosages (not WGS where matching will be limited). Related to #283

smlmbrt

Error: results missing for single sample

6

### Description of the bug In the current dev build, the report is made, but it does not contain any columns except for SUM: ``` sampleset IID PGS SUM Z_MostSimilarPop...

Fiwx

Problematic harmonzied scorefile for PGS004700 crashes pgs_calc 2.0.0-alpha5

2

### Discussed in https://github.com/PGScatalog/pgsc_calc/discussions/278 Originally posted by **bgulko** April 16, 2024 runing pgs_calc with --trait_efo EFO_0005140 accesses PGS004700 (grch38/singularity), which generates error and halts the pipeline in combine_scorefiles When I...

smlmbrt

Fail of run_ancestry process INTERSECT_THINNED

16

### Description of the bug I am having a bug during run_ancestry calculation. Any idea what does it mean? PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (R01axy)' Caused by: Process `PGSCATALOG_PGSCALC:PGSCALC:ANCESTRY_PROJECT:INTERSECT_THINNED (R01axy)` terminated with an error...

mireklzicar

Will use new python-based intersect variants to implement MAF/missingness filters to define variants in the target dataset that are PCA-eligible: https://github.com/PGScatalog/pygscatalog/blob/match_intersect/pgscatalog.match/src/pgscatalog/match/cli/intersect_cli.py

smlmbrt

Integrate OmicsPred

1

### Description of feature Ensure that pgsc_calc works with [OmicsPred](https://www.omicspred.org) scoring files. Would be ideal to use pre-combined score files (see #64) and be able to specify ID/platform on the...

smlmbrt