This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Manually creating a valid VCF File

Hi there,

I'm trying to manually make a valid vcf file for some indels. I've managed to do so for single nucleotide variations, but indels have failed so far. I check the validity with vcf-validator (https://github.com/EBIvariation/vcf-validator). My output error file is the following for the vcf file I've included as an image here:

According to the VCF specification, the input file is not valid

Error: The header line does not start with the mandatory columns: CHROM, POS, ID, REF, ALT, QUAL, FILTER and INFO. This occurs 1 time(s), first time in line 6.
Warning: A valid 'reference' entry is not listed in the meta section. This occurs 1 time(s), first time in line 6.
Error: Chromosome is not a string without whitespaces, optionally wrapped with angle brackets (<>). This occurs 1 time(s), first time in line 7.

VCF file:

image of VCF file

Any guidance would be greatly appreciated!

vcf-validator vcf
• 1,188 views • link
updated by Bastien Hervé Bastien Hervé • written by Sara • Sara

Sara : Please do not post screenshots of text content. It is difficult for users to help (by copy pasting things from text). Use 101010 button to format the text as code to keep it monospaced and in right visual format.

• 0 views • link
written by GenoMax GenoMax

1 answer

Can we have an example of what is working, to compare too ?

If you do it manually, don't use whitespace between entities, use tabulation.

As you did not include any fasta reference, maybe vcf-validator does not allow chromosome written chr10 but only 10

• 0 views • link
written by Bastien Hervé Bastien Hervé

Thanks so much Bastien! I added the fasta file and made sure I used tabs. It works now!

• 0 views • link
written by Sara • Sara

Log in to answer this question.

More posts like this