uploding VCF file to CADD and Ensemb

Question

[Eliza]

Hi, I have a CSV file that contains the columns: CHROM, POS,REF, and ALT

I want to convert this CSV file to a VCF file to upload to CADD:https://cadd.gs.washington.edu/score and,Ensembl https://www.ensembl.org/Tools/VEP to get SNP annotations. this is my code in python spyder to convert :

import csv
import gzip
# Open the CSV file
with open('C:/Users/agns1/Downloads/genetics/data/df_vcf.csv', 'r') as csvfile:
    reader = csv.reader(csvfile)
    # Skip the header row
    next(reader)
    # Open the VCF file for writing
    with open('data.vcf', 'w') as vcffile:
        # Write the VCF file header
        vcffile.write('##fileformat=VCFv4.2\n')
        vcffile.write('#CHROM\tPOS\tREF\tALT\n')
        # Iterate through the CSV rows
        for row in reader:
            # Write the VCF data
            vcffile.write(row[0] + '\t' + row[1] + '\t'  + row[2] + '\t' + row[3]  + '\n')

the file that i get looks like this and has name data.vcf :

BUT Ensembl and CADD "say" the the format of the file is not correct, and i dont understand why since it is a VCF file (or how to fix this problem ) thank you:)

Answer 1

[Pierre Lindenbaum]

You have

#CHROM POS REF ALT

while a vcf MUST HAVE

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO

you can use '.' for the missing fields.

[Eliza]

can i add this column and they would be just empty? in the CADD websote it says :"It is sufficient to provide the first 5 columns of a VCF file without header, as all other information than CHROM, POS, REF, ALT will be ignored anyway. "

[Pierre Lindenbaum]

It is sufficient to provide the first 5

so ID is missing....

[Eliza]

got this error from ensmble when I loaded the corrected file:"exiting the program. The input file appears to be unsorted. Please sort by chromosome and by location and re-submit." should I order the data by ascending Chrom and inside the chrom by acs POS

[Ben_Ensembl]

Hi Eliza - yes, that is correct.