gaow

KING step reports an error when no related individuals are detected

1

Also an issue reported from Travyse. We need to consider this and make the step more robust.

There are two annotation databases we can use for psichomic: one shipped from the software itself and the other generated via SUPPA on our GTF reference. What puzzled me was...

VCF_QC raise error when lacking certain tags

1

Report from Travyse: in the VCF_QC step the VCF file that I was provided lacks the DP tag, so the pipeline quits on error.

Make sure SesameData annotation includes probe information

2

From a discussion between @hsun3163 and @yuqimiao it seems like currently we are not using probe information from SesameData object. We need to make sure that is the case. I...

Including missing data imputation and normalization @yuqimiao

eg, APEX, stephenslab, PEER. There is an offending line `su -` at the beginning of these files.

How to best save per gene data

2

We need to save per gene data for workflows with SuSiE, mvSuSiE, MR-MASH and FUSION. Currently we have two ways to save it 1. in RDS format for R based...

A reminder to myself to document it here: https://cumc.github.io/xqtl-pipeline/code/data_preprocessing/phenotype/gene_annotation.html#overview

When to intersect samples among genotype, phenotype and covariates

6

## Complication Genotype and covariates are possibly shared across all studies and phenotypes are unique to each one. Sometimes the overlap is large and the few non-overlapping samples are negligible...

`LDtools` package extension

6

@changebio moving our slack discussions here. ## Objective It is non-trivial to handle all these data merger and region extraction etc for integrative analysis. I would like to revisit and...