SNP's and Gene?

Question

[imgapgenomika]

How to translate SNPs into gene? And gene in phenotype in bovine? Is it a program I can use?

[Joe]

How to translate SNPs into gene?

What does this mean? This makes no sense.

[imgapgenomika]

Thank Joe! I have a list of 17 individuals, father, mother and children. Each individual has 35,000 known SNPs. How to know the genes of these SNPs?

[Joe]

Please just stop here and go back and add much more information to your question. We don't know what format your data is in, so we can't answer this in its current form.

You also asked for bovine phenotypic information, what has this to do with your human samples? Misunderstood, my mistake.

[imgapgenomika]

SNP Name    Chr Position    Sample ID   Allele1 - Forward   Allele2 - Forward   Allele1 - Top   Allele2 - Top   Allele1 - AB    Allele2 - AB    Log R Ratio B Allele Freq   GC Score    GT Score    SNP Theta   R   X   Y   X Raw   Y Raw   CNV Value   CNV Confidence  
ARS-BFGL-BAC-11044  1   12805406    00-Touro    C   C   G   G   B   B   0.0695  0.9986  0.8378  0.8149  [T/C]   0.973   0.983   0.040   0.943   1217    5143    2.0

This is the genotyping of a bovine (Bos indicus). I want to know how to read the result, can you help me?

[WouterDeCoster]

PLEASE EDIT YOUR ORIGINAL QUESTION WITH THIS NEW INFORMATION.

[Emily]

What reference genome were the SNPs called against?

[imgapgenomika]

Hi Emily! Genome of Bos indicus cattle.

[Emily]

What was the accession of the genome assembly?

[imgapgenomika]

Emily! Sorry I did not understand your question?

[Emily]

Then you have a problem. If you don't know what genome these variants were called on then you have no way of interpreting them. Species name is not enough, you need an accession number, usually a short combination of letters and numbers that indicates exactly which version of the genome you were using. If you don't know that then you don't know what is at chromosome 1, position 12805406, so there is nothing you can do with that data.

Imagine that I told you to find an important quote on page 100 of Oliver Twist. Here are all the versions of Oliver Twist that I can buy from Amazon. See if you can find the quote on page 100.

[imgapgenomika]

SNP Name    Chr Position    Sample ID   Allele1 - Forward   Allele2 - Forward   Allele1 - Top   Allele2 - Top   Allele1 - AB    Allele2 - AB    Log R Ratio B Allele Freq   GC Score    GT Score    SNP Theta   R   X   Y   X Raw   Y Raw   CNV Value   CNV Confidence  
ARS-BFGL-BAC-11044  1   12805406    00-Touro    C   C   G   G   B   B   0.0695  0.9986  0.8378  0.8149  [T/C]   0.973   0.983   0.040   0.943   1217    5143    2.0 .

Emily, this is a small sample from the result of an Illumina cattle genotyping, GGP 35K. How do I have to analyze it?

[Emily]

You have already shown us what the data looks like. I am asking you a different question: what is the genome assembly?

You need to read the specs given to you by Illumina. Somewhere in there it will say what genome assembly the variant location is listed as. Once you have that, you need to convert your data into VCF and run it through a variant annotation tool, like the VEP. If the genome assembly is not one that is included already, you will need to get a FASTA file and a GTF of gene annotation to match the assembly.

Next time: find out what data you're going to get out and how you're going to interpret it BEFORE buying an expensive Illumina product.

[imgapgenomika]

Thank you, Emily! I'll try...( My name is : Kélia Margarida Barros Freire, Brazil :) [e-mail] )