Last updated: 2019-03-09

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Knit directory: threeprimeseq/analysis/

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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd e69f2d3 Briana Mittleman 2019-03-09 add new GWAS overlap
html 55a488c Briana Mittleman 2019-03-09 Build site.
Rmd ea54d47 Briana Mittleman 2019-03-09 add new GWAS overlap

Full GWAS catelog from the table browser. There are 56248699 lines in this file:

/project2/gilad/briana/genome_anotation_data/hg19.GWASCatelog.allsnps

First I want to subset this to a bed file to use. I also want to subset only to SNPs.

Columns: bin chrom chromStart chromEnd name score strand refNCBI refUCSC observed molType class valid avHet avHetSE func locType weight exceptions submitterCount submitters alleleFreqCount alleles alleleNs alleleFreqs bitfields

sed 's/^chr//' /project2/gilad/briana/genome_anotation_data/hg19.GWASCatelog.allsnps  > /project2/gilad/briana/genome_anotation_data/hg19.GWASCatelog.allsnps.bed

overlapSNPsGWAS_fixed.py

def main(infile, outfile):
    gwas_file=open("/project2/gilad/briana/genome_anotation_data/hg19.GWASCatelog.allsnps.bed","r")
    gwas=pybedtools.BedTool(gwas_file)
    snps_file=open(infile, "r")
    snps=pybedtools.BedTool(snps_file)
    snpOverGWAS=snps.intersect(gwas, wa=True,wb=True)
    snpOverGWAS.saveas(outfile)

if __name__ == "__main__":
    import sys
    import pybedtools
    infile=sys.argv[1]
    outfile=sys.argv[2]
    main(infile, outfile)

run_overlapSNPsGWASFixed_proc.sh

#!/bin/bash

#SBATCH --job-name=run_overlapSNPsGWASFixed_proc
#SBATCH --account=pi-yangili1
#SBATCH --time=5:00:00
#SBATCH --output=run_overlapSNPsGWASFixed_proc.out
#SBATCH --error=run_overlapSNPsGWASFixed_proc.err
#SBATCH --partition=broadwl
#SBATCH --mem=10G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env


python overlapSNPsGWAS_fixed.py  "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/AllOverlapSnps.bed" "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap_processed/GWASoverlapped_AllOverlapSnps.bed"

This analysis gives 9k overlaps with 7k uniq snps. of (53135726 uniq snps)

This makes more sense.

I want to only look at relevent GWAS for LCLs

I will also need to compare to random snps. (i can use my matched snps/find those in LD)



sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.2.0 Rcpp_1.0.0      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.3 git2r_0.24.0    magrittr_1.5    evaluate_0.13  
 [9] stringi_1.3.1   fs_1.2.6        whisker_0.3-2   rmarkdown_1.11 
[13] tools_3.5.1     stringr_1.4.0   glue_1.3.0      xfun_0.5       
[17] yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6 knitr_1.21