/
callMolQTLS.Rmd
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callMolQTLS.Rmd
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---
title: "Call aditional molecular QTLs"
author: "Briana Mittleman"
date: "9/25/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
I will use this analysis file to recall the other molecular QTLs using the same VCF files I am using for the APAqtls. This is important because we want to overlap QTLs called with the same genotype information.
* **processed (WASP+normalized) 4sU-seq (30m)**
* **processed (WASP+normalized) 4sU-seq (60m) **
* **processed (WASP+normalized) RNA-seq (Pickrell)**
* **processed (WASP+normalized) RNA-seq (GEUVADIS)**
* **processed (WASP+normalized) ribo-seq**
* **LiftOver from (Battle et al., 2015) protein **
I am download the processed data from http://eqtl.uchicago.edu/jointLCL/ and putting it in /project2/gilad/briana/threeprimeseq/data/molecular_phenos.
The protein file is already in the format needed for fastQTL. I need to change the headers to include the NA before the individuals.I will need to use:
`export PATH=/project/gilad/software/midway1/qtltools-1.0:$PATH`
##RiboQTL
```bgzip phenotypes.bed && tabix -p bed phenotypes.bed.gz```
To index the file for the program.
I will create a python script that adds the NA to the individuals.
```{bash, eval=F}
def main(inF, outF):
infile= open(inF, "r")
fout = open(outF,'w')
for i, line in enumerate(infile):
if i == 0:
linelist=line.split()
for i, item in enumerate(linelist):
if i > 3:
linelist[i]="NA" + item
fout.write(" ".join(linelist) + '\n' )
else:
fout.write(line)
fout.close()
if __name__ == "__main__":
import sys
inF = sys.argv[1]
outF= sys.argv[2]
main(inF, outF)
```
Next step is to get the PCs to use as covariates in the analysis.
https://qtltools.github.io/qtltools/
This package is in /project/gilad/software/midway1/ and was installed by Peter Carbaneto from the RCC. I can add this to my path with:
```
export PATH=/project/gilad/software/midway1/qtltools-1.0:$PATH
```
I am going to use the QTLtools pca function. I need to run this on midway1.
```{bash, eval=F}
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.PC.txt
#keep top 5 PCs for analysis
head -n 6 fastqtl_qqnorm_ribo_phase2.fixed.bed.PC.txt.pca > fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs.txt.pca
```
I then make a samples file wit the head of the PCA file. Remove 19192,19193 from sample file
I need to make 1 vcf file with all of the chroms to run this.
riboQTL.nom.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=riboQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=riboQTL.nom.out
#SBATCH --error=riboQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_ribo_phase2.fixed.nominal.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/samples.txt
done
```
problem chr in pheno file and not in vcf
```{bash,eval=F}
sed 's/^chr//' fastqtl_qqnorm_ribo_phase2.fixed.bed > fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed
```
try changing /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs.txt.pca first part of header to id like in the FastQTL site. and use tr to make it tap deliminated from " "
riboQTL.perm.sh
```{bash, eval=F}
#!/bin/bash
#SBATCH --job-name=riboQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=riboQTL.perm.out
#SBATCH --error=riboQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.bed.5PCs_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_ribo_phase2.fixed.noChr.bed.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_ribo_phase2.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/samples.txt
done
```
I can process these to by generalizing my script from the apaQTLsAllInd.Rmd
##eqtl
I need to remove the Chr and add the NA.
fastqtl_qqnorm_RNAseq_phase2.txt
```{bash,eval=F}
python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.txt
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt
bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt
tabix /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz
#midway1
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.PC.txt
#keep top 5 PCs for analysis
head -n 6 fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.PC.txt.pca > fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC.txt.pca
less fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca
```
I want to create a script that checks the samples in the file and then makes a samples.txt file if they are in the VCF.
First create a file with the names of the individuals in the vcf files. /project2/gilad/briana/YRI_geno_hg19/vcf.samples.txt
create_molQTLSamplefile.py
```{bash, eval=F}
#infile is the pheno PCA file (because it is not zipped)
#outfile is the samples for that pheno if they are in the vcf samples
def main(inF, outF):
vcf_samp=open("/project2/gilad/briana/YRI_geno_hg19/vcf.samples.txt", "r")
for line in vcf_samp:
vcf_list=line.split()
infile= open(inF, "r")
fout = open(outF,'w')
for i, line in enumerate(infile):
if i ==0:
mol_samples=line.split()[1:]
final_samps=[]
for i in mol_samples:
if i in vcf_list:
final_samps.append(i)
fout.write("\n".join(final_samps))
if __name__ == "__main__":
import sys
inF = sys.argv[1]
outF= sys.argv[2]
main(inF, outF)
```
Run in the code dir:
```{bash,eval=F}
python create_molQTLSamplefile.py ../data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca ../data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt
```
rnaQTL.nom.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=rnaQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=rnaQTL.nom.out
#SBATCH --error=rnaQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseq_phase2.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt
done
```
rnaQTL.perm.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=rnaQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=rnaQTL.perm.out
#SBATCH --error=rnaQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseq_phase2.Samples.txt
done
```
##ProteinQTL
http://eqtl.uchicago.edu/jointLCL/fastqtl_qqnorm_prot.txt.gz
```{bash,eval=F}
python /project2/gilad/briana/threeprimeseq/code/addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.txt
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt
bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt
tabix -p bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz
#midway1
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.PC.txt
#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC.txt.pca
less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca
```
```{bash,eval=F}
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt
```
protQTL.nom.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=protQTL.nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=protQTL.nom.out
#SBATCH --error=protQTL.nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_prot.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt
done
```
protQTL.perm.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=protQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=protQTL.perm.out
#SBATCH --error=protQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_prot.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_prot.fixed.noChr.SAMP.txt
done
```
##RNAgQTL
fastqtl_qqnorm_RNAseqGeuvadis_phase2.txt.gz
```{bash,eval=F}
python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.txt
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt
bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt
tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz
#midway1
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.PC.txt
#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC.txt.pca
less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca
```
```{bash,eval=F}
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt
```
RNAgQTL.nuc.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RNAgQTL.nuc
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=RNAgQTL.nuc.out
#SBATCH --error=RNAgQTL.nuc.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_RNAseqGeuvadis.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt
done
```
RNAgQTL.perm.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=RNAgQTL.perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=RNAgQTL.perm.out
#SBATCH --error=RNAgQTL.perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --permute 1000 --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_RNAseqGeuvadis.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_RNAseqGeuvadis_phase2.fixed.noChr.SAMP.txt
done
```
##4su 60
```{bash,eval=F}
python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.txt
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt
bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt
tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz
#midway1
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.PC.txt
#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC.txt.pca
less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca
```
```{bash,eval=F}
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt
```
4su60QTL_nom.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=4su60QTL_nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su60QTL_nom.out
#SBATCH --error=4su60QTL_nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su60.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt
done
```
4su60QTL_perm.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=4su60QTL_perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su60QTL_perm.out
#SBATCH --error=4su60QTL_perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_4su60.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_60_phase2.fixed.noChr.SAMP.txt
done
```
##4su 30
```{bash,eval=F}
python addNAphenohead.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.txt /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.txt
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.txt > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt
bgzip /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt
tabix -p bed -f /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz
#midway1
QTLtools pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --scale --center --out /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.PC.txt
#keep top 5 PCs for analysis
head -n 6 /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.PC.txt.pca > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC.txt.pca
less /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC.txt.pca | tr " " "\t" > /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca
```
```{bash,eval=F}
python create_molQTLSamplefile.py /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.SAMP.txt
```
4su30QTL_nom.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=4su30QTL_nom
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su30QTL_nom.out
#SBATCH --error=4su30QTL_nom.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/nom/fastqtl_qqnorm_4su30.fixed.nominal.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.SAMP.txt
done
```
4su30QTL_perm.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=4su30QTL_perm
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=4su30QTL_perm.out
#SBATCH --error=4su30QTL_perm.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
for i in $(seq 1 30)
do
/home/brimittleman/software/bin/FastQTL/bin/fastQTL.static --vcf /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf.gz --cov /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.5PC_tab.txt.pca --bed /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.txt.gz --out /project2/gilad/briana/threeprimeseq/data/molecular_QTLs/perm/fastqtl_qqnorm_4su30.fixed.perm.chunk$i.out --chunk $i 30 --window 5e4 --include-samples /project2/gilad/briana/threeprimeseq/data/molecular_phenos/fastqtl_qqnorm_4su_30_phase2.fixed.noChr.SAMP.txt
done
```