Generating fasta from VCF with only the variant

Question

[the_cowa]

Hi Stars,

I did an alignment and from that, I called the variant (VCF). So my question is how I can convert that vcf into fasta with the only predicted variant, not consensus. I know usually for consensus we will do it with GATK Fasta Alternate Reference or BCF tools.

Excepted fasta out as like this (If there is no variation, that position must be noted with N)

>Seq1
NNNNNANNNNTNNNNNNGNNNNNNNNNC

Any ideas?

[Ram]

What is the purpose of this exercise?

[the_cowa]

I am trying to generate a new gene sequence from an known reference, so I am not interested the same reference sequence

[Ram]

You should be able to write some code to fetch reference sequences and apply any variants, as long as they are in HGVS nomenclature. Read the python hgvs package documentation for a basic understanding of how you can interact with posedit components.