I'm trying to generate a fasta file from a reference including variants in a vcf file. I'm using bcftools and it works.
My problem is that I would like to create a fasta where only the mutated positions are showing and the wild type ones are representes as -.
So for example, if I have a mutation in position 3, the fasta should look like:
--T----
Is it possible?
Sure there possibly can be several ways to do the task (but I don't know myself), however, why would you want to do that?
One can see if there are mutations or SNPs in any sequence only if there are more that one sequence, or generally a multiple sequences in aligned format. And if you want to get the nucleotide which shows a change, manual inspection is always the best. And if you want to present your research/finding in a journal or anywhere, it is always recommended and logical to present in multiple sequence alignment format, where you can present the mutation against the reference.
I know GenerateAltAlleleFasta
https://gatkforums.broadinstitute.org/gatk/discussion/1493/generatealtallelefasta
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