Getting A Table Of Genotypes (Snps) Into A Genome Browser

Question

[Yannick Wurm]

I work with a non-model organism which is absent from online genome browsers. I have genotypes at 5000 loci for 100 haploid individuals. This is currently in the form of a table in R. Something like this:

           ind1  ind2  ind3     [...]   ind100    
locus 1      A     G     A                 M       (M = genotype unknown)
locus 2      C     C     M                 T
locus 3      G     M     C                 G
   [...]
locus 5000   -     T     -                 T

I performed a crude GWAS-type analysis (my individuals are split into 2 groups; such analysis is easy with haploids). Now I want to visualize genotypes in a genome browser (Savant or IGV or something). The easiest seeems to be if I output so that I get one "track" with all individuals from 1 group; and a second "track" with individuals from the other group.

Which output format is my best bet? Googling seems to suggest that VCF is most appropriate. But I remain very confused by the format specifications: can I make one VCF per group? Will I then be able to see for each group, how many individuals have which genotype? Or would another format be better?

How would a line from such a file look like?

Thanks in advance, Yannick

Answer 1

[Mary]

I think you could do this pretty quickly with WebGBrowse. The file only requires a little bit of structure and you could see the things you need pretty quickly, I think. There are GFF3 files samples and you should fine plenty of other examples around of GBrowse style variation tracks.

[Khader Shameer]

Mary, Nice one. Thanks for the tip !