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I'm looking to use the software DIYABC 2.1.0 to apply approximate bayesian computing (ABC) to some resequenced data that I have.

The resequenced data is in FASTA format however, and the software requires an SNP datafile format (.snp). How do I generate such a file from FASTA formatted data? Is it possible?

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  • $\begingroup$ I don't know either piece of software. Hopefully, someone will have written a utility to do the conversion you need, or maybe there is a set of utilities, so that you can convert from format A, to B, to C, etc. However, sometimes you have to write your own genetic data file conversion program (in Python, Perl, etc.--whatever you like). It's probably conceptually easy--you're just rearranging or recoding the same data--although the routines can require some care. If you know enough to get started, but get stuck along the way, Stackoverflow.com would be relevant. Maybe none of this is news. $\endgroup$ – Mars Oct 29 '15 at 5:22
  • $\begingroup$ You will have to detect SNPs. You can get the vcf by aligning your resequenced fastA to the reference genome (or previously sequenced genome) and use a Variant Calling method of your liking. Then there is this tool to convert vcf to the required .snp file: github.com/loire/vcf2DIYABC.py $\endgroup$ – skymningen Oct 29 '15 at 8:10
  • $\begingroup$ @Mars That's very helpful, thank you. I'm very much a novice, so any input is appreciated! $\endgroup$ – Will Perry Nov 1 '15 at 23:30
  • $\begingroup$ @skymningen Great, I shall try and produce that intermediate vcf file. I did try using PGDSpider to convert the files, but there was obviously something else that had to be done. Cheers! $\endgroup$ – Will Perry Nov 1 '15 at 23:33

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