chris1221 / impute

Automated imputation pipeline for arbitrary dataset and reference panels.

Hi there, I'm Chris.

I am currently a lead scientist at Deep Genomics in Toronto. My work involves using machine learning and AI to identify causal drug targets from human genetics data. I previously completed my DPhil working with Gerton Lunter and Thomas Milne at the University of Oxford. Check out my website for a breakdown of previous projects and repositories of interest.

impute's Issues

Chr 0, 24:27

What are these? Ask Jen

CONFIG file

Need to make one that works for both BASH and R

Check duplicated SNPs to see if INDELs are causing problems

Perl sink error

rename portion is causing empty files, this may potentially impact previous steps.

Issues Remaining

January 12th Meeting

• Email Rachel, Meghan Jen, Dr Knight about plans for transfer
• X, Y are reasonable
• Are there custom SNPs in chromosome 0 or 24:27?
• Not going to do mitochondria

ChrX imputation

Review the procedure for imputing chr X; it's different

Amalgamate scripts into makefile

E.g.

Params in .impute.config, then simply make impute.

Or impute --file ${FILE} --ref ${REF} --out ${OUT} --... if as a complete script.

QC

• MAF < 1%
• INFO < 0.4