VCF To FASTA

Question

[Myo Naung]

Hi,

Do anyone know how to convert VCF files into FASTA files such as using R ?

Myo

[finswimmer]

Hello Myo Naung ,

what do you expect by this "conversion"? A vcf file contains information about differences compared to a given reference. What you can do is: Take your reference sequence and integrate your variants. This is called a consensus sequence. bcftools consensus is one tool that can do this (if this is what you want to do).

fin swimmer

[Myo Naung]

Hello fin swimmer,

Thanks for the suggestions. What I would like to do is to calculate neutrality statistics like Tajima's D, and there I would like to see TD values of variant sites related to conserved regions. Not sure I can do directly from vcf.

Myo

[seta]

Hi fin swimmer, creating consensus reference genome for a specific human population can be considered as a alternative for de novo genome assembly?

Answer 1

[MatthewP]

Hello, vcftools has a command vcf-consensus which can convert VCF to FASTA file if you got the reference. Command like:

cat ref.fa | vcf-consensus your_file.vcf.gz > out.fa

[Ram]

Please do not use convert when dealing with data formats with non-equivalent information content. You cannot convert VCF to FASTA, you can combine alternate allele information from a VCF into a reference FASTA to get FASTA that incorporates a specific percentage of the ALT alleles into itself.

[Myo Naung]

Thanks, @MattweP. I will have a look

[davidenoma]

I tried this command and I got: Applied 0 variants.