check the variations incorporated to consensus fasta by vcf-consensus

Question

[iraun]

Hi all,

I'm trying to check the variations inserted by vcf-consensus in my new consensus fasta. I mean, I have a vcf file and the reference, and I have used vcf-consensus to produce a new fasta. I have a script that checks the length of the indels in my vcf, and the length of fasta files. So, I have assumed that:

length of my reference - deletions length + insertions length = new reference length

But the calculation gives me different results, and this is why I'm here. So, there is a way to check out which variations have been inserted by vcf-consensus? Maybe it performs some filter I don't know... My vcf only contains homozygous variations.

Any suggestion?

Thanks in advance

Answer 1

[Cytosine]

The formula you gave sounds about right, and I'm not really sure why you get incongruencies...

You could try writing your own script, that modifies a reference fasta according to an associated vcf file.

With that you can compare the "black-box" vcf-consensus and your own script if they produce identical results.