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
1 answer
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.
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