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  • fastPHASE to Haploview

    Hi everyone!

    Is anyone familiar with Haploview? If so, could you tell me whether it is possible to input fastPHASE output file formats into Haploview?
    If not, I have my information in the following structure (unphased SNP matrix):
    locus1 locus2 locus3 etc.
    ind1 allele A G A T
    ind1 allele B C G T

    ind2 allele A G G A
    ind2 allele B G G A

    ind3 allele A C G C
    ind3 allele B C A C
    etc.

    What would be the easiest way to input this SNP table into Haploview?

    Thank you for help and any suggestions!

  • #2
    The Haploview file format documentation is quite verbose, and should get you most of the way to working out how to massage the fastPhase format into one of the accepted formats.

    The quickest way to do this would probably be to hunt around for a program to convert fastPHASE format to Linkage format -- while the "Phased Haplotypes" format looks the closest to your data, it requires a bit more complex manipulation to sort out the heterozygous genotypes. To go from fastPHASE to Linkage (assuming your example is correct), you would delete the marker line, add in dummy phenotype columns, then interleave the alleles on each line so that you end up with one individual per line:

    Code:
    1 ind1 0 0 0 0  G C  A G  T T
    2 ind2 0 0 0 0  G G  G G  A A
    3 ind3 0 0 0 0  C C  G A  C C
    etc.
    You also need a marker file, which shows the location of the markers in the order they appear in the columns of the Linkage file:

    Code:
    locus1  123568
    locus2  160189
    locus3  491249
    etc.
    Hmm, AG, then GA? I thought it was unphased....

    Anyway, read the file format documentation for Haploview -- you'll probably learn something I haven't told you here.

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