VEP annotated VCF conversion into TSV/Text
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
1 answer
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
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Hamid Ghaedi
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yussab •
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yussab •
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You have tagged this with
bcftoolsalready. Have you read the documentation for the split-vep plugin?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 ....
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.
The columns are in the same order that you specified them. Multiple values will be delimited by a comma unless you specify
--duplicatewhich will generate one line per transcript.Should I apply into this: bcftools +split-vep test/split-vep.vcf -f -duplicate '%CHROM:%POS %CSQ\n' -d -A tab