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 in a given number of bins (100 variants by default)
- Running VEP on the split VCFs in parallel
- Merging VEP outputs into a single file
The nextflow pipeline requires Nextflow (tested on 21.10.0).
The following config files are used and can be modified depending on user requirements:
- VEP config file
cp vep_config/vep.ini.template vep_config/vep.ini-
Nextflow config file
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 \
--vcf <path-to-vcf> \
-profile <standard or lsf or slurm> --vcf VCF Sorted and bgzipped VCF. Alternatively, can also be a directory containing VCF files
--bin_size INT Number of variants used to split input VCF into multiple jobs. Default: 100
--vep_config FILENAME VEP config file. Alternatively, can also be a directory containing VEP INI files. Default: vep_config/vep.ini
--cpus INT Number of CPUs to use. Default: 1
--outdir DIRNAME Name of output directory. Default: outdir
--output_prefix PREFIX Output filename prefix. The generated output file will have name <output_prefix>_VEP.vcf.gz.
NOTE: Do not use this parameter if you are expecting multiple output files.
--skip_check [0,1] Skip check for tabix index file of input VCF. Enables use of cache with -resume. Default: 0 bgzip -c $PWD/examples/clinvar-testset/input.vcf > $PWD/examples/clinvar-testset/input.vcf.gz
nextflow \
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.
work/singularity/quay.io-biocontainers-bcftools-*.img 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