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  • GATK multisample vcf to BayeScan input

    Hi all,

    I am trying to convert a "multi-sample (population)" vcf file from GATK obtained using a "joint genotyping workflow" for a non-model organism. Since we want to do population studies, I need to convert the .vcf file to a format used as input to a tool such as BayeScan (http://cmpg.unibe.ch/software/BayeScan/)..

    I tried using file conversion tools such as PGDSpider "http://www.cmpg.unibe.ch/software/PGDSpider/". which gives me an output but for only for the 1st sample (population) !!!

    I am attaching my input and output files for reference..

    Appreciate any feedback,

    regards,

    Nandan

    Any other tools to do Fst outlier analysis using a "vcf" file with multiple samples?
    Attached Files

  • #2
    Hi Nandan,

    I hope you fixed your problem since that time.
    Anyway, I think you need to convert your file in the PGDSpider own format (PGD), then concert to Bayescan format. I was having the same problem of conversion for different input format type, and it was resolved that way.

    In short, convert that way in 2 steps:
    VCF -> PGD -> Bayescan

    Best,
    Alex

    Comment


    • #3
      PGDSpider doesn't name the loci in its list, so I used the
      Code:
      make_bayescan_input.py
      script from The Simple Fool's Guide to Population Genomics via RNA-Seq available at http://sfg.stanford.edu/Scripts.zip

      There are instructions for the script at the following webpage:
      http://sfg.stanford.edu/SNP.html you just need to scroll down to "3)FST Outliers" to find the instructions once you are on the page.

      Best,
      Gopo

      Comment

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