Question: Getting A Table Of Genotypes (Snps) Into A Genome Browser
gravatar for Yannick Wurm
7.6 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

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

ADD COMMENTlink written 7.6 years ago by Yannick Wurm2.3k
gravatar for Mary
7.6 years ago by
Boston MA area
Mary11k wrote:

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.

ADD COMMENTlink written 7.6 years ago by Mary11k

Mary, Nice one. Thanks for the tip !

ADD REPLYlink written 7.6 years ago by Khader Shameer18k
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