The nextflow pipeline aims to run VEP faster utilising simple parallelisation. It is deployable on an individual Linux machine or on computing clusters running lsf or slurm (not tested). The process can be summarised briefly by the following steps:
- Splitting the VCF chromosome-wise
- Running VEP on chromosome-wise VCFs in parallel
- Merging VEP outputs into a single file
The nextflow pipeline requires the following dependencies:
- Nextflow (tested on 21.10.0)
- Singularity (tested on 3.7)
Singularity images are required in order to run the following tools:
- bcftools
- VEP
The singularity images can be fetched by running:
./setup-images.shThe following config files are used and can be modified depending on user requirements:
- VEP config file
cp nf_config/vep.ini.template nf_config/vep.ini-
Nextflow config file
nf_config/nextflow.confighas the default options for running the pipeline. The file can be modified to change the default options or override them using command line options
Currently supported profiles for executors are standard (local), LSF and SLURM (untested!). As mentioned SLURM is untested at present, if you are running this pipeline on a slurm compute cluster and encounter problems, please contact us with details (raise a ticket on the github) and we can investigate. NB: If no profile is mentioned, the pipeline takes the standard profile.
nextflow run workflows/run_vep.nf \
-C nf_config/nextflow.config \
--vcf <path-to-vcf> \
--chros 1,2 \
-profile <standard or lsf or slurm> --vcf VCF VCF that will be split. Currently supports sorted and bgzipped file
--outdir DIRNAME Name of output dir. Default: outdir
--vep_config FILENAME VEP config file. Default: nf_config/vep.ini
--chros LIST_OF_CHROS Comma-separated list of chromosomes to generate. i.e. 1,2,..., Default: 1,2,...X,Y,MT
--cpus INT Number of CPUs to use. Default 1.NB: File paths are expected to be absolute paths.
bgzip -c $PWD/examples/clinvar-testset/input.vcf > $PWD/examples/clinvar-testset/input.vcf.gz
nextflow -C nf_config/nextflow.config \
run workflows/run_vep.nf \
--vcf $PWD/examples/clinvar-testset/input.vcf.gz \
-profile lsfThe above commands start the pipeline and generate the output file upon completion.
singularity-images/bcftools.sif bcftools view \
-H outdir/merged-file.vcf.gz \
-r 1Expected result
1 925952 1019397 G A . . ALLELEID=1003021;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.11:g.925952G>A;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=SAMD11:148398;MC=SO:0001583|missense_variant;ORIGIN=1;CSQ=A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding|||||||||||4360|1|cds_start_NF|HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|2/14||||101|11|4|G/E|gGg/gAg|||1||HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|2/5||||71|11|4|G/E|gGg/gAg|||1|cds_end_NF|HGNC|HGNC:28706,A|upstream_gene_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000609207|retained_intron|||||||||||4936|-1||HGNC|HGNC:53933,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding|2/14||||1057|548|183|G/E|gGg/gAg|||1||HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding|1/11||||11|11|4|G/E|gGg/gAg|||1|cds_start_NF|HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding|1/13||||11|11|4|G/E|gGg/gAg|||1|cds_start_NF|HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding|1/10||||11|11|4|G/E|gGg/gAg|||1|cds_start_NF|HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding|2/14||||1057|548|183|G/E|gGg/gAg|||1||HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding|1/12||||11|11|4|G/E|gGg/gAg|||1|cds_start_NF|HGNC|HGNC:28706,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding|1/13||||11|11|4|G/E|gGg/gAg|||1|cds_start_NF|HGNC|HGNC:28706
1 930139 1125147 C T . . ALLELEID=1110865;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.11:g.930139C>T;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=SAMD11:148398;MC=SO:0001627|intron_variant;ORIGIN=1;CSQ=T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding|||||||||||173|1|cds_start_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||2/13||||||||||1||HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding||2/4||||||||||1|cds_end_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||2/13||||||||||1||HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||1/10||||||||||1|cds_start_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||1/12||||||||||1|cds_start_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||1/9||||||||||1|cds_start_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||2/13||||||||||1||HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||1/11||||||||||1|cds_start_NF|HGNC|HGNC:28706,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||1/12||||||||||1|cds_start_NF|HGNC|HGNC:28706