VCF tab to FASTA Alignment Script

I’m not sure if anyone will find this useful, but I’m making available a tiny script I wrote to convert VCF tab files (output from VCFtoolsvcf-to-tab utility) to FASTA alignments. Essentially it just concatenates your SNPs. I found this useful as a quick sanity check when working with massive SNP datasets: I converted my VCF files to VCF tabular files, then used this script to make a quick FASTA alignment so I could generate a fast neighbor joining tree. The script is available on Google Code here:


Let me know if you ever use it!

  1. Hi! Nice script!

    Is there a way you clould also import a fasta file of the variants instead of the IUPAC notation for the allele?

    • Thanks, Norman! I’m not sure I’m following what you’re asking. The input would be SNPs in FASTA format, and what would the output be?

  2. Nice script!
    I noticed it generates a *.tab_clean file which deleted all the indels before convert to fasta. Is there a way to also include indels in the final output?
    Many thanks!


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