README.md

In noahrose/vcf2eqtl: eQTL detection from a transcriptome reference

vcf2eqtl

A pipeline for eQTL detection from a transcriptome reference

• The pipeline uses a simple counts matrix and VCF input file
• Both of these file types are standard parts of RNA-Seq experiments

Install (R 3.3.1 or greater):

source("https://bioconductor.org/biocLite.R")
biocLite(c('devtools','DESeq2','limma','VariantAnnotation','qvalue'))
library(devtools)
install_github('whitlock/OutFLANK')
install_github('noahrose/vcf2eqtl')

Call variants with freebayes and filter for biallelic SNPs

freebayes -f ref.fa *.bam > fb.vcf
cat fb.vcf \
| vcfnulldotslashdot \
| grep -vF './.' \
| vcffilter -f "TYPE = snp & QUAL > 30 & AF > 0.1 & AF < 0.9 & NUMALT = 1" -g "DP > 10" \
> biallelic_snps.vcf

You will also need a gene expression counts matrix of the same format used for DESeq

• Many ways to do this, including:
• samtools idxstats
• htseq-count
• Trinity/RSEM
• StringTie
• etc...

Then load into R

expr <- read.delim('expr.txt',row.names=1)
vcf <- 'biallelic_snps.vcf'
metadata<-read.delim('meta.txt')
pops=metadata$pops
vcf2eqtl(vcf,expr,pops)

noahrose/vcf2eqtl documentation built on May 23, 2019, 9:30 p.m.