apaQTL GWAS overlap

Last updated: 2018-11-09

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Unstaged changes:
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    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/coloc_apaQTLs_protQTLs.Rmd
    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/flash2mash.Rmd
    Modified:   analysis/overlapMolQTL.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/swarmPlots_QTLs.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   code/Snakefile

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File	Version	Author	Date	Message
Rmd	489bf91	Briana Mittleman	2018-11-09	code for plink r2
html	0428c8c	Briana Mittleman	2018-10-29	Build site.
Rmd	42d0e3d	Briana Mittleman	2018-10-29	add gwas overlap to index

In this analysis I want to see if APAqtls show up in the GWAS catelog. I then want to see if they explain different signal then overlappnig the eQTLs.

I can use my significant snp bed file from /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps to overlap with the GWAS catelog. First I can look at direct location then I will use an LD cutoff to colocalize.

/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed
/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed

The downloaded GWAS catalog from the UCSD table browser.

/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.txt

I will make this into a bed format to use with pybedtools.

-Chrom -start -end -name -score

fin=open("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.txt", "r")
fout=open("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.bed","w")

for num, ln in enumerate(fin):
  if num > 0: 
    line=ln.split("\t")
    id_list=[line[4],line[5], line[14]]
    start=int(line[2])
    end=int(line[3])
    id=":".join(id_list)
    chr=line[1][3:]
    pval=line[16]
    fout.write("%s\t%d\t%d\t%s\t%s\n"%(chr,start, end, id, pval)
fout.close()

Pybedtools to intersect my snps with catelog /project2/gilad/briana/threeprimeseq/data/GWAS_overlap

output dir:

import pybedtools
gwas=pybedtools.BedTool("/project2/gilad/briana/genome_anotation_data/hg19GwasCatalog.sort.bed")
nuc=pybedtools.BedTool("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed")
tot=pybedtools.BedTool("/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed") 

nucOverGWAS=nuc.intersect(gwas, wa=True,wb=True)
totOverGWAS=tot.intersect(gwas,wa=True, wb=True)

#this only results in one overlap:  
nucOverGWAS.saveas("/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/nucFDR10overlapGWAS.txt")

Problem: I see this snp but it is assoicated with a different gene. I need to think about gene and snp overlap.

I can see if this snp is an eqtl.

16:30482494

eqtl=read.table(file = "../data/other_qtls/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.out")
eqtl_g= read.table("../data/other_qtls/fastqtl_qqnorm_RNAseqGeuvadis.fixed.perm.out")

This snp is not in either of these files. I will check for them in the nominal results.

grep 16:30482494   /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.out


grep 16:30482494   /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.out

LD structure

https://vcftools.github.io/man_latest.html –vcf (vcf file) –geno-r2 –out (prefix) vcf tools is on midway 2 “module load vcftools”

I can use the snp files I created for the chromHMM analysis.

/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed
/project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnp/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed

I can use awk to get the first and third column.

awk '{print $1 ":" $3}' /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Nuclear.sort.bed > /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Nuclear.txt

awk '{print $1":"$3}' /project2/gilad/briana/threeprimeseq/data/perm_APAqtl_trans/sigSnps/ApaQTLsignificantSnps_10percFDR_Total.sort.bed > /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt

testLD_vcftools_totQTL.sh


#!/bin/bash

#SBATCH --job-name=testLD_vcftools_totQTL.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=testLD_vcftools_totQTL.out
#SBATCH --error=testLD_vcftools_totQTL.err
#SBATCH --partition=broadwl
#SBATCH --mem=16G
#SBATCH --mail-type=END

module load vcftools

vcftools --gzvcf chr1.dose.vcf.gz  --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt --out /project2/gilad/briana/YRI_geno_hg19/chr1.totQTL.LD --geno-r2

/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/TotalApaQTL_LD

/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/NuclearApaQTL_LD

Now run this for all chr in both fractions.

LD_vcftools.sh

#!/bin/bash

#SBATCH --job-name=LD_vcftools.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=LD_vcftools.out
#SBATCH --error=rLD_vcftools.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load vcftools

for i  in {1..22};
do
vcftools --gzvcf /project2/gilad/briana/YRI_geno_hg19/chr${i}.dose.vcf.gz  --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/TotalApaQTL_LD/chr${i}.totQTL.LD --geno-r2 --min-r2 .8
done


for i  in {1..22};
do
vcftools --gzvcf /project2/gilad/briana/YRI_geno_hg19/chr${i}.dose.vcf.gz  --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Nuclear.txt --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/NuclearApaQTL_LD/chr${i}.nucQTL.LD --geno-r2 --min-r2 .8
done

This doesnt give very many more snps. Let me try this with Tony’s vcf files from the larger panel of LCLs.

Try it with the –hap-r2 argument.

LD_vcftools.hap.sh

#!/bin/bash

#SBATCH --job-name=LD_vcftools.hap.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=LD_vcftools.hap.out
#SBATCH --error=rLD_vcftools.hap.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load vcftools

for i  in {1..22};
do
vcftools --gzvcf /project2/gilad/briana/YRI_geno_hg19/chr${i}.dose.vcf.gz  --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/TotalApaQTL_LD/chr${i}.totQTL.hap.LD --hap-r2--min-r2 .8
done


for i  in {1..22};
do
vcftools --gzvcf /project2/gilad/briana/YRI_geno_hg19/chr${i}.dose.vcf.gz  --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Nuclear.txt --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/NuclearApaQTL_LD/chr${i}.nucQTL.hap.LD --hap-r2 --min-r2 .8
done

still not a lot of snps.

testLDGeu_vcftools_totQTL.sh


#!/bin/bash

#SBATCH --job-name=testLDGeu_vcftools_totQTL.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=testLDGeu_vcftools_totQTL.out
#SBATCH --error=testLDGeu_vcftools_totQTL.err
#SBATCH --partition=broadwl
#SBATCH --mem=16G
#SBATCH --mail-type=END

module load vcftools

vcftools --gzvcf /project2/yangili1/LCL/genotypesYRI.gen.txt.gz   --snps  /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/geuvadis.totQTL.LD --geno-r2

Error: Insufficient sites remained after filtering

vcf2Plink.sh

#!/bin/bash

#SBATCH --job-name=vcf2Plink
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=vcf2Plink.out
#SBATCH --error=vcf2Plink.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load vcftools

for i  in {1..22};
do
vcftools --gzvcf /project2/gilad/briana/YRI_geno_hg19/chr${i}.dose.vcf.gz --plink --chr ${i} --out /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr${i}
done

Try with plink:
I will use the ped and map files: –ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr$i.ped –map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chri.map

–ld-snp-list /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt

–r2

–ld-window-r2 0.20.8 testPlink_r2.sh

#!/bin/bash

#SBATCH --job-name=testPlink_r2
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=testPlink_r2.out
#SBATCH --error=testPlink_r2.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load plink

plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr22.ped  --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr22.map --r2  --ld-window-r2 0.8 --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/plinkYRI_LDchr22

This gives me 77,000 pairs. I will run this on all of the chromosomes then subset by snps i have QTLs for.

RunPlink_r2.sh

#!/bin/bash

#SBATCH --job-name=RunPlink_r2
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunPlink_r2.out
#SBATCH --error=RunPlink_r2.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load plink


for i  in {1..22};
do
plink --ped /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr${i}.ped  --map /project2/gilad/briana/YRI_geno_hg19/plinkYRIgeno_chr${i}.map --r2  --ld-window-r2 0.8 --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/plinkYRI_LDchr${i}
done

I can now subset these files for snps in the /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Total.txt and /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_Nuclear.txt files using a python script.

This script will take a fraction and chromosome.

subset_plink4QTLs.py


    
def main(genFile, qtlFile, outFile):
  #convert snp file to a list: 
  def file_to_list(file):
    snp_list=[]
    for ln in file:
      snp=ln.strip()
      snp_list.append(snp)
    return(snp_list)

  gen=open(genFile,"r")
  fout=open(outFile, "w")
  qtls=open(qtlFile, "r")
  qtl_list=file_to_list(qtls)
  for ln in gen:
      snp=ln.split()[2]
      if snp in qtl_list:
          fout.write(ln)
  fout.close()
    

if __name__ == "__main__":
    import sys
    chrom=sys.argv[1]
    fraction=sys.argv[2]
    genFile = "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/plinkYRI_LDchr%s.ld"%(chrom)
    outFile= "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/%sApaQTL_LD/chr%s.%sQTL.LD.geno.ld"%(fraction,chrom,fraction)
    qtlFile= "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_%s.txt"%(fraction)
    main(genFile, qtlFile, outFile)

Run this for all chr in a bash script:

run_subset_plink4QTLs.sh

#!/bin/bash

#SBATCH --job-name=run_subset_plink4QTLs
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=run_subset_plink4QTLs.out
#SBATCH --error=run_subset_plink4QTLs.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env


for i  in {1..22};
do
python subset_plink4QTLs.py ${i} "Total"
done

for i  in {1..22};
do
python subset_plink4QTLs.py ${i} "Nuclear"
done

This results in 385 more snps for the nuclear QTLs and 54 more for the total.

I want to try this method on the bigger panel from Tonys work.

vcf2Plink_geu.sh

#!/bin/bash

#SBATCH --job-name=vcf2Plink_geu
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=vcf2Plink_geu2.out
#SBATCH --error=vcf2Plink_geu2.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load vcftools

for i  in {1..22};
do
vcftools --gzvcf /project2/yangili1/LCL/geuvadis_genotypes/GEUVADIS.chr${i}.hg19_MAF5AC.vcf.gz --plink --chr ${i} --out /project2/gilad/briana/YRI_geno_hg19/geu_plinkYRIgeno_chr${i}
done

RunPlink_Geu_r2.sh

#!/bin/bash

#SBATCH --job-name=RunPlink_geu_r2
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=RunPlink_geu_r2.out
#SBATCH --error=RunPlink_geu_r2.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END

module load plink


for i  in {1..22};
do
plink --ped /project2/gilad/briana/YRI_geno_hg19/geu_plinkYRIgeno_chr${i}.ped  --map /project2/gilad/briana/YRI_geno_hg19/geu_plinkYRIgeno_chr${i}.map --r2  --ld-window-r2 0.8 --out /project2/gilad/briana/threeprimeseq/data/GWAS_overlap/geu_plinkYRI_LDchr${i}
done

Update the python selection script for geu results.
subset_plink4QTLs_geu.py


    
def main(genFile, qtlFile, outFile):
  #convert snp file to a list: 
  def file_to_list(file):
    snp_list=[]
    for ln in file:
      snp=ln.strip()
      snp_list.append(snp)
    return(snp_list)

  gen=open(genFile,"r")
  fout=open(outFile, "w")
  qtls=open(qtlFile, "r")
  qtl_list=file_to_list(qtls)
  for ln in gen:
      snp=ln.split()[2]
      if snp in qtl_list:
          fout.write(ln)
  fout.close()
    

if __name__ == "__main__":
    import sys
    chrom=sys.argv[1]
    fraction=sys.argv[2]
    genFile = "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/geu_plinkYRI_LDchr%s.ld"%(chrom)
    outFile= "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/%sApaQTL_LD_geu/chr%s.%sQTL.LD.geno.ld"%(fraction,chrom,fraction)
    qtlFile= "/project2/gilad/briana/threeprimeseq/data/GWAS_overlap/ApaQTLsigSNPpos_%s.txt"%(fraction)
    main(genFile, qtlFile, outFile)

run_subset_plink4QTLs_geu.sh

#!/bin/bash

#SBATCH --job-name=run_subset_plink4QTLs_geu
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=run_subset_plink4QTLs_geu.out
#SBATCH --error=run_subset_plink4QTLs_geu.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env


for i  in {1..22};
do
python subset_plink4QTLs_geu.py ${i} "Total"
done

for i  in {1..22};
do
python subset_plink4QTLs_geu.py ${i} "Nuclear"
done

Session information

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

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_1.1.1   Rcpp_0.12.19      digest_0.6.17    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1

apaQTL GWAS overlap

Briana Mittleman

10/26/2018

LD structure

Session information