MattWellie commented 2 years ago

Fixes

N/A

Proposed Changes

helper script for generating family data from sample-metadata:
1. Pedigree
2. Pedigree in PLINK format
3. sample -> participant reverse lookup

Checklist

[ ] Related Issue created
[x] Tests covering new change
[x] Linting checks pass

Misc

Early version of this script (#1) made some incorrect assumptions about the relationship between participants and samples. This version allows for a 1 -> n relationship, and all possible variations will be present in the final PED file

Use of the de novo functionality in Hail required the generation of a Pedigree in PLINK format, so that has been added as an option. I've confirmed that Peddy also accepts PLINK and .ped files interchangeably, so .fam is the new default for this application.

The mapping back from samples to participants is required when formatting results for presentation back to clinical analysts, so creation of that mapping has been included as a step here.

MattWellie commented 2 years ago

welp, rebased this after the recent merge to main and it's gone insane

MattWellie commented 2 years ago

Closing as superseded, suggested changes made in a separate (cleaner) merge

populationgenomics / automated-interpretation-pipeline

Generate pedigree #26

Fixes

Proposed Changes

Checklist

Misc