LDregress.Rmd

---
title: "LD score regression"
author: "Briana Mittleman"
date: "1/30/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

LD score regression with apaQTLs and multiple myeloma? 

https://www.nature.com/articles/s41467-018-04989-w

QTLs:

Region around permuted snps. 500bp

try a few different

PAS:

maybe 1000 base pairs around each PAS.

bed file chrom start and end. - use CHR

-b cells: lymphocite 


GWAS atlas 

http://www.computationalmedicine.fi/data#Cytokine_GWAS

GWAS from Phenix= /project2/yangili1/zpmu/GWAS_loci/27863252 

sle_Vyse_chr1-22.txt.gz 

RA_GWASmeta_TransEthnic_v2.txt.gz

http://www.nealelab.is/uk-biobank - myeloma and luekemias 

HG 19 LD scores 

- change to numpy 1.16 

https://github.com/bulik/ldsc

03,05,06,07

/project2/yangili1/zpmu/ldsc/scripts