Sep 21, 2020
VEPextended
- Israel Aguilar Ordoñez1
- 1Instituto Nacional de Medicina Genómica (INMEGEN)
- Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights
External link: https://github.com/Iaguilaror/nf-VEPextended
Protocol Citation: Israel Aguilar Ordoñez 2020. VEPextended. protocols.io https://dx.doi.org/10.17504/protocols.io.bkhvkt66
Manuscript citation:
Aguilar-Ordoñez I, Pérez-Villatoro F, García-Ortiz H, Barajas-Olmos F, Ballesteros-Villascán J, González-Buenfil R, Fresno C, Garcíarrubio A, Fernández-López JC, Tovar H, Hernández-Lemus E, Orozco L, Soberón X, Morett E (2021) Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PLoS ONE 16(4): e0249773. doi: 10.1371/journal.pone.0249773
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 31, 2020
Last Modified: September 21, 2020
Protocol Integer ID: 41237
Abstract
'VEPextended' is a tool, implemented in Nextflow, that annotates called variants using Variant Effect Predictor (VEP) and additional plugins that implement functionalities, that are not included in variation API.
All steps described are mk modules of code that will be done automatically through Nextflow pipeline.
Guidelines
Instalation
Download VEPextended from Github repository:
Compatible OS*:
* VEPextended may run in other UNIX based OS and versions, but testing is required.
Software Requirements:
Software
bcftools
NAME
Software
htslib
NAME
Software
ensembl-vep
NAME
Software
Nextflow
NAME
Materials
Pipeline Inputs
- A compressed vcf file with extension '.vcf.gz', which must have a TABIX index with .tbi extension, located in the same directory as the vcf file.
Note(s): INFO must cointain AC
Example line(s):
##fileformat=VCFv4.2
##FILTER=
##GATKCommandLine.ApplyRecalibration.2=##INFO=
##INFO=
##contig=
##contig=
##contig=
##bcftools_viewCommand=view --compression-level 0 --output-type z --min-ac 1 --threads 1 ./test/data/sample.vcf.gz;
#CHROM POS ID REF ALT QUAL FILTER INFO
chr22 30000353 . G T . PASS AC=107;AF_mx=0.708;AN=150;DP=883;nhomalt_mx=39
- *_dbSNP.vcf.gz: A reference dbSNP b152 file, that contains rsID of variants.
- Pre-scored files for SNVs and InDels compressed and indexed provided from CADD. Availables in
- Liftedover of gnomAD release 2.1.1 to GRCh38
- Coverages from gnomAD v 2.1.1
Dataset
gnomad.genomes.coverage.summary.bed.gz
NAME
- GWAS association for SNVs (no haplotypes) compiled by iaguilar from GWAScat database at Spring 2019
- Coordinates for every pre-miRNA, mature miRNA and seed region from miRBase v22.
- _coverages.bed.gz: contains covergage of your sample.
- genotype - drug associations from PGKB
Before start
Test
To test VEPextended's execution using test data, run:
./runtest.sh
Your console should print the Nextflow log for the run, once every process has been submitted, the following message will appear:
======
VEP annotator: Basic pipeline TEST SUCCESSFUL
======
VEPextended results for test data should be in the following file:
test/results/_pos1_rejoin_chromosomes/sample.filtered.untangled_multiallelics.anno_dbSNP_vep.vcf.gz
Usage
To run VEPextended go to the pipeline directory and execute:
nextflow run vep-annotator.nf --vcffile [--output_dir path to results ] [-resume]
For information about options and parameters, run:
nextflow run vep-annotator --help
Pre-processing
Pre-processing
Filter VCF
Remove the variants that did not have any copy of the alternative allele.
Note
a) Filter and remove when there was not an alternative allele in the VCF file.vcf.gz, to only conserve found variants.
b) Compress the filtered file using one thread for compression.
c) Make and index output file using the filtered and compressed file.
Dependencies:
Software
bcftools
NAME
Extract chromosomes
Extract variants per chromosome vcf file that have at least one variant.
Note
a) Using the index of the compressed vcf file, list the chromosomes names.
b) If there is at least one variant per chromosome, separate variants per chromosome.
Dependencies:
Software
bcftools
NAME
Software
htslib
NAME
Split chromosomes
Split in chunks a vcf file, keeping its format.
Note
a) Save the header of a vcf in a temporary file.
b) Save the body of a vcf in a temporary file.
c) Make chunks of the body of the vcf file.
d) Add the header to each body chunk.
Dependencies:
Software
bcftools
NAME
Core-processing
Core-processing
Untangle multiallelic
Split multiallelic sites.
Note
a) Separate multiallelic sites and conserve vcf format.
b) Do not print bcftools version.
Dependencies:
Software
bcftools
NAME
Annotate rsID
Annotate rsID to each variant in ID column of a VCF.
Note
a) Make a Reference file with a define range.
b) Compress input file.
c) Annotate rsID in the compressed input file using a Reference.
Dependencies:
Software
bcftools
NAME
Software
htslib
NAME
Vep Extended
Annotate variants with Variant Effector Predictor tool (VEP). For more information about, seeVEP
Dependencies:
Software
ensembl-vep
NAME
Pos-processing
Pos-processing
Rejoin chromosomes
Concatenate annotated chunks in a single vcf file.
Dependencies:
Software
bcftools
NAME
Software
htslib
NAME
Final Output:
Expected result
VCF file with only variants of each chromosome from the input.
Example line(s):
##fileformat=VCFv4.2 #CHROM POS ID REF ALT AC AN DP AF_mx nhomalt_mx Allele Consequence IMPACT SYMBOL Gene Feature_type Feature BIOTYPE EXON INTRON HGVSc HGVSp cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation DISTANCE STRAND FLAGS VARIANT_CLASS SYMBOL_SOURCE HGNC_ID CANONICAL TSL APPRIS CCDS ENSP SWISSPROT TREMBL UNIPARC SOURCE GENE_PHENO SIFT PolyPhen DOMAINS HGVS_OFFSET HGVSg AF AFR_AF AMR_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF MAX_AF MAX_AF_POPS CLIN_SIG SOMATIC PHENO PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE GeneHancer_type_and_Genes gnomADg gnomADg_AC gnomADg_AN gnomADg_AF gnomADg_DP gnomADg_AC_nfe_seu gnomADg_AN_nfe_seu gnomADg_AF_nfe_seu gnomADg_nhomalt_nfe_seu gnomADg_AC_raw gnomADg_AN_raw gnomADg_AF_raw gnomADg_nhomalt_raw gnomADg_AC_afr gnomADg_AN_afr gnomADg_AF_afr gnomADg_nhomalt_afr gnomADg_AC_nfe_onf gnomADg_AN_nfe_onf gnomADg_AF_nfe_onf gnomADg_nhomalt_nfe_onf gnomADg_AC_amr gnomADg_AN_amr gnomADg_AF_amr gnomADg_nhomalt_amr gnomADg_AC_eas gnomADg_AN_eas gnomADg_AF_eas gnomADg_nhomalt_eas gnomADg_nhomalt gnomADg_AC_nfe_nwe gnomADg_AN_nfe_nwe gnomADg_AF_nfe_nwe gnomADg_nhomalt_nfe_nwe gnomADg_AC_nfe_est gnomADg_AN_nfe_est gnomADg_AF_nfe_est gnomADg_nhomalt_nfe_est gnomADg_AC_nfe gnomADg_AN_nfe gnomADg_AF_nfe gnomADg_nhomalt_nfe gnomADg_AC_fin gnomADg_AN_fin gnomADg_AF_fin gnomADg_nhomalt_fin gnomADg_AC_asj gnomADg_AN_asj gnomADg_AF_asj gnomADg_nhomalt_asj gnomADg_AC_oth gnomADg_AN_oth gnomADg_AF_oth gnomADg_nhomalt_oth gnomADg_popmax gnomADg_AC_popmax gnomADg_AN_popmax gnomADg_AF_popmax gnomADg_nhomalt_popmax gnomADg_cov gwascatalog gwascatalog_GWASC_trait gwascatalog_GWASC_pvalue gwascatalog_GWASC_study clinvar clinvar_CLNDN clinvar_CLNSIG clinvar_GENEINFO clinvar_CLNDISDB miRBase pharmgkb_drug pharmgkb_drug_PGKB_annid pharmgkb_drug_PGKB_gene pharmgkb_drug_PGKB_chem pharmgkb_drug_PGKB_phencat chr22 16132524 . G C 27 156 1962 0.173 3 C intergenic_variant MODIFIER . . . . . . . . . . . . . . . . . . SNV . . . . . . . . . . . . . . . . chr22:g.16132524G>C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . chr22 27840687 . G T 69 156 2311 0.442 18 T