Believe analysis

Web: https://jinghuazhao.github.io/Believe

CSD3 location

  • ~/rds/pre_qc_data/believe
  • ~/rds/rds-jmmh2-post_qc_data/believe

  • ~/rds/rds-jmmh2-post_qc_data/believe/reference_files/genetic/pLOF/pLOF_annotation_may_2022

  • TOPMed imputation data by Regeneron for the full ~72k participants. genotype/imputed/*Freeze_Two.GxS.TOPMED_dosages* (.pgen-GT files, .pgen-HDS files and .bgen files pending).

  • PCs (counterpart to the sequenced variants, genotype/genomewide/plink/aug_2023??).

A growing list of scripts.

0_utils.sh
1_desc.sh
2_gcta.sb

0. Utilities

0_utils.sh reads information such as Olink Parquet and SomaLogic adat files.

1. Descriptive analysis

1_desc.sh is to extract data and to protoype some canonical options for handling relatedness in the study.

2. GCTA work

2_gcta.sb contains various approaches for the analysis.

A. URLs