VCF to FASTA

Question

[page2]

Hello,

I need to convert .vcf files from 1000Genomes into FASTA files while maintaining phasing. I currently am doing this more or less manually using excel. We tried using Galaxy but couldn't figure out how to maintain the phasing from the vcf.

I am wondering if there is a fast and easy way to do this that I haven't found?

Unfortunately I don't know any programming, otherwise I'm sure this would be much easier.

Thank you!

[Jorge Amigo]

there are several biostars entries addressing this issue: check Introducing Known Mutations (From A Vcf) Into A Fasta File, Standard Genome Plus Vcf To Variant Genome or New Fasta Sequence From Reference Fasta And Variant Calls File? for instance. GATK's FastaAlternateReferenceMaker is what I usually go for.

Answer 1

[Matt Shirley]

Erik Garrison (freebayes author) has a small tool to make a consensus FASTA using any phased variants in a VCF. Take a look here: https://github.com/ekg/vcflib/blob/master/src/vcf2fasta.cpp

Answer 2

[castelli]

You may use vcfx. It creates a fasta file (two sequences per sample) using a reference sequence and replacing each variable site on the right location. It supports indels. Take a look here: www.castelli-lab.net/apps/vcfx

[Matt Shirley]

Seems like interesting software, but please consider releasing the source code instead of a pre-compiled binary. The readme also states that the license is Creative Commons, so I'm not sure that there's any reason to limit end users to a binary blob. Some people would also complain about the requirement to register using an email address/password (do you really need to register accounts or could you just collect optional emails?) when we already have too many logins to remember. I can't evaluate the functionality of the software either as the publication is not open-access. In light of this I wouldn't trust the results from this program because I have no way to know anything about it's inner workings or quality.