Convert GWAS summary statistics to VCF

Tool to map GWAS summary statistics to VCF/BCF with on-the-fly harmonisation to a supplied reference FASTA

Produces GWAS-VCF with version 1.0 of the specification

Citation

Lyon, M.S., Andrews, S.J., Elsworth, B. et al. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol 22, 32 (2021). https://doi.org/10.1186/s13059-020-02248-0

Quick start

Use web interface http://vcf.mrcieu.ac.uk

Run locally

Either run directly on a UNIX host or using Docker containerisation (recommended)

Download

git clone git@github.com:MRCIEU/gwas2vcf.git
cd gwas2vcf

Native

Requires Python v3.8

python3 -m venv env
source env/bin/activate
pip install -r requirements.txt
pip install git+git://github.com/bioinformed/vgraph@v1.4.0#egg=vgraph
python main.py -h

Docker

Build docker image

docker build -t gwas2vcf .

Run

docker run \
-v /path/to/fasta:/path/to/fasta \
--name gwas2vcf \
-it gwas2vcf:latest \
python main.py -h

Reference FASTA

# GRCh36/hg18/b36
wget http://fileserve.mrcieu.ac.uk/ref/2.8/b36/human_b36_both.fasta
wget http://fileserve.mrcieu.ac.uk/ref/2.8/b36/human_b36_both.fasta.fai

# GRCh37/hg19/b37
wget http://fileserve.mrcieu.ac.uk/ref/2.8/b37/human_g1k_v37.fasta
wget http://fileserve.mrcieu.ac.uk/ref/2.8/b37/human_g1k_v37.fasta.fai

# GRCh38/hg38/b38
wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta
wget https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai

dbSNP

# GRCh37/hg19/b37
wget http://fileserve.mrcieu.ac.uk/dbsnp/dbsnp.v153.b37.vcf.gz .
wget http://fileserve.mrcieu.ac.uk/dbsnp/dbsnp.v153.b37.vcf.gz.tbi .

# GRCh38/hg38/b38
wget http://fileserve.mrcieu.ac.uk/dbsnp/dbsnp.v153.hg38.vcf.gz .
wget http://fileserve.mrcieu.ac.uk/dbsnp/dbsnp.v153.hg38.vcf.gz.tbi .

Running the tests

Unit tests:

cd gwas2vcf
python -m pytest -v test

Usage

usage: main.py [-h] [-v] [--out OUT] [--data DATA] --ref REF [--dbsnp DBSNP] --json JSON [--id ID] [--cohort_controls COHORT_CONTROLS]
               [--cohort_cases COHORT_CASES] [--csi] [--log {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--alias ALIAS]

Map GWAS summary statistics to VCF/BCF

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --out OUT             Path to output VCF/BCF. If not present then must be specified as 'out' in json file
  --data DATA           Path to GWAS summary stats. If not present then must be specified as 'data' in json file
  --ref REF             Path to reference FASTA
  --dbsnp DBSNP         Path to reference dbSNP VCF
  --json JSON           Path to parameters JSON
  --id ID               Study identifier. If not present then must be specified as 'id' in json file
  --cohort_controls COHORT_CONTROLS
                        Total study number of controls (if case/control) or total sample size if continuous. Overwrites value if present in json
                        file.
  --cohort_cases COHORT_CASES
                        Total study number of cases. Overwrites value if present in json file.
  --csi                 Default is to index tbi but use this flag to index csi
  --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the logging level
  --alias ALIAS         Optional chromosome alias file

Additional parameters are passed through a JSON parameters file using --json <param.json>, see param.py for full details and below example. Note that field columns start at 0.

Example

Assuming the GWAS summary stats have a hg19/b37 chromosome name & position you can use these files:

• RefGenomeFile
• DbSnpVcfFile
• alias.txt

# obtain test gwas summary stats
wget https://raw.githubusercontent.com/MRCIEU/gwas2vcfweb/master/app/tests/data/example.1k.txt

# create json parameters file
{
  "chr_col": 0,
  "pos_col": 1,
  "snp_col": 2,
  "ea_col": 3,
  "oa_col": 4,
  "beta_col": 5,
  "se_col": 6,
  "ncontrol_col": 7,
  "pval_col": 8,
  "eaf_col": 9,
  "delimiter": "\t",
  "header": true,
  "build": "GRCh37"
}

# map to GWAS-VCF
SumStatsFile=/data/example.1k.txt
RefGenomeFile=/data/human_g1k_v37.fasta
ParamFile=/data/params.json
DbSnpVcfFile=/data/dbsnp.v153.b37.vcf.gz
VcfFileOutPath=/data/out.vcf
ID="test"

python /app/main.py \
--data ${SumStatsFile} \
--json ${ParamFile} \
--id ${ID} \
--ref ${RefGenomeFile} \
--dbsnp ${DbSnpVcfFile} \
--out ${VcfFileOutPath} \
--alias /app/alias.txt

Working with GWAS-VCF

See below examples of working with GWAS-VCF. Let us know if you have other use cases through the issues page!

Parsing libraries

See R and Python libraries for reading GWAS summary statistics in GWAS-VCF

Command-line manipulation

The following examples require:

• bcftools
• gatk
• htslib

Please cite the relevant tool(s) if you use these examples.

Filter

Extract genome-wide significant variants

The LP field is -log10(P), 7.3 is approx 5e-8

bcftools filter \
-i 'FORMAT/LP > 7.3' \
-o output.vcf \
file.vcf.gz

Extract variants by gene

Requires annotation by Ensembl (see below)

bcftools filter \
-i 'INFO/ENSG_ID == "ENSG00000198670"' \
file.vcf.gz

Extract variants by pathway

Requires annotation by Reactome (see below)

bcftools filter \
-i 'INFO/Reactome_ID == "R-HSA-3000171"' \
file.vcf.gz

Select genome region for further analysis

bcftools filter \
-r 1:1000000-2000000 \
-o output.vcf.gz \
input.vcf.gz

Annotate

Add variant frequency

# download 1000 genomes phase 3 (hg19/GRCh37) allele frequencies and index
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi 

# annotate GWAS-VCF with 1kg allele frequencies
bcftools annotate \
-a ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz \
-c AF \
-O z \
-o output.vcf.gz \
input.vcf.gz

Add gene/pathway annotations

Download and merge input files

# download ensembl-to-position mapping and sort by ensgId
curl ftp://ftp.ensembl.org/pub/grch37/release-87/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz | \
gzip -dc | \
awk -F"\t|:|;|=" '$3=="gene" && $1 >= 1 && $1 <= 22 {print $11"\t"$1"\t"$4"\t"$5}' | \
sort -k1,1 > Ensembl2Position.sorted.txt

# download ensembl-to-pathway mapping and sort by ensgId
curl https://reactome.org/download/current/Ensembl2Reactome.txt | \
grep "Homo sapiens" | \
cut -s -f1,2 | \
sort -k1,1 > Ensembl2Reactome.sorted.txt

# merge tables by ensgId, sort, compress and index
join \
-t $'\t' \
--check-order \
Ensembl2Position.sorted.txt \
Ensembl2Reactome.sorted.txt | \
awk -F"\t" '{print $2"\t"$3-1"\t"$4"\t"$5}' | \
sort -k1,1V -k2,2n -k3,3n | \
bgzip -c > reactome.bed.gz
tabix -p bed reactome.bed.gz

# sort, compress and index ensembl-to-position mapping
awk -F"\t" '{print $2"\t"$3-1"\t"$4"\t"$1}' Ensembl2Position.sorted.txt | \
sort -k1,1V -k2,2n -k3,3n  | \
bgzip -c > ensembl.bed.gz
tabix -p bed ensembl.bed.gz

Annotate GWAS-VCF with gene ID

# annotate GWAS-VCF
bcftools annotate \
-a ensembl.bed.gz \
-c CHROM,FROM,TO,ENSG_ID \
-h <(echo '##INFO=<ID=ENSG_ID,Number=.,Type=String,Description="Ensembl gene ID">') \
-o output.vcf.gz \
-O z \
-l ENSG_ID:unique \
input.vcf.gz

Annotate GWAS-VCF with Reactome ID

# annotate GWAS-VCF
bcftools annotate \
-a reactome.bed.gz \
-c CHROM,FROM,TO,Reactome_ID \
-h <(echo '##INFO=<ID=Reactome_ID,Number=.,Type=String,Description="Reactome ID">') \
-o output.vcf.gz \
-O z \
-l Reactome_ID:unique \
input.vcf.gz

Convert

Export to NHGRI-EBI GWAS catalog format

# map to GWAS catalog format
bcftools query \
-e 'ID == "."' \
-f '%ID\t[%LP]\t%CHROM\t%POS\t%ALT\t%REF\t%AF\t[%ES\t%SE]\n' \
gwas.vcf.gz | \
awk 'BEGIN {print "variant_id\tp_value\tchromosome\tbase_pair_location\teffect_allele\tother_allele\teffect_allele_frequency\tbeta\tstandard_error"}; {OFS="\t"; if ($2==0) $2=1; else if ($2==999) $2=0; else $2=10^-$2; print}' > gwas.tsv

# validate file using [ss-validate](https://pypi.org/project/ss-validate)
ss-validate -f gwas.tsv

Liftover

Map genomic coordinates to another genome build (liftover)

This procedure requires a chain file which contains the chromosome base-position mapping between two genome builds

# download chain file
wget http://fileserve.mrcieu.ac.uk/ref/chains/b36tob37.chain
wget http://fileserve.mrcieu.ac.uk/ref/chains/b37tob36.chain
wget http://fileserve.mrcieu.ac.uk/ref/chains/b37tohg18.chain
wget http://fileserve.mrcieu.ac.uk/ref/chains/b37tohg19.chain
wget http://fileserve.mrcieu.ac.uk/ref/chains/hg18tob37.chain
wget http://fileserve.mrcieu.ac.uk/ref/chains/hg19toHg18.chain

# perform liftover
 gatk LiftoverVcf \
--INPUT input.vcf.gz \
--OUTPUT output.vcf.gz \
--REJECT rejected.vcf.gz \
--CHAIN file.chain \
--REFERENCE_SEQUENCE target.fasta \
--RECOVER_SWAPPED_REF_ALT false 

Merge

Combine multiple GWAS summary stats into a single file

This is useful for distributing QTL/molecular phenotype GWAS

bcftools merge \
-O z \
-o merged.vcf.gz \
*.vcf.gz

Validate

Check the file format is valid

gatk ValidateVariants \
-V input.vcf.gz \
-R ref.fasta \
--validation-type-to-exclude ALLELES