VEP annotated VCF conversion into TSV/Text

Question

[Nai]

VEP annotated VCF has CHROM, POS, REF, ALT , INFO, FORMAT : genotype. I would like to convert this VCF as tab delimited file where I can get INFO column will be tab delimited

Like Chr Pos ID Ref Alt Filter INFO ALLELE Consequence IMPACT SYMBOL Gene Feature_type Feature BIOTYPE EXON INTRON HGVS HGVSp cDNA_position|CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND FLAGS VARIANT CADD etc All colums values will be splitted as tab separated

[LChart]

You have tagged this with bcftools already. Have you read the documentation for the split-vep plugin?

[Nai]

When I am doing with bcftools, it is showing only columns CHROM, REF, ALt etcc...I am not getting to split the other columns with headers like: ALLELE VARIANT FEATURE_type PROTEIN gnomADg_AF ....

[Nai]

I tried this bcftools +split-vep test/split-vep.vcf -f '%CHROM:%POS %CSQ\n' -d -A tab

But this command does not give any header information. I need header also like which column value belongs to which column.

[LChart]

The columns are in the same order that you specified them. Multiple values will be delimited by a comma unless you specify --duplicate which will generate one line per transcript.

[Nai]

Should I apply into this: bcftools +split-vep test/split-vep.vcf -f -duplicate '%CHROM:%POS %CSQ\n' -d -A tab

Answer 1

[yussab]

Hi Nai,

there are several ways to achieve this task, if you're familiar with R use this script Please let me know if you found it useful and remeber to mark as answered if it's ok :) Best regards, Youssef

#START

library(vcfR);

library(ensemblVEP);

library(dplyr)


#VEP Read files

vep_file = "VCF_vep.vcf"

vep_workir="~/results/02_vep/"

setwd(vep_workir)



vep_vcfr <- read.vcfR( vep_file, verbose = FALSE )

vep_header <- data.frame(vep_vcfr@meta)

vep_variants <- data.frame(vep_vcfr@fix)

vep_gt <- data.frame(vep_vcfr@gt)



#Parse into a GRanges and include the 'VCFRowID' column.

vep_ens <- readVcf(vep_file, "hg19")

csq_vep <- parseCSQToGRanges(vep_ens)

csq_vep <- data.frame(csq_vep)



VEP <- cbind.data.frame(vep_variants,csq_vep,vep_gt)

write.csv(VEP, file= output_path)

#END

[Nai]

I have Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10 r83330). When installing ensemblVEP, it is not supported to latest version. Kindly help me to get something else.

[yussab]

Use conda to get all installation

[yussab]

Hi Nai, I suggest you to get the installation done with conda and try this script, it'll save you a look of time ;) I've already tried most of the other methods, including a script that I wrote myself