Illumina Snp Array

Question

[Demis001]

The SNP table in Illumina GenomeStudio contains the same SNP (eg A/C or A/G for all 97 samples) per marker for all samples if the call was made for a all samples. How that would be possible? Is there a way to convert Genotype call to the SNP call for each samples (AB -> T/C, AA -> A/G ...etc)?

Here is a few lines from the "SNP table" from GenomeStudio. See the last three column. The SNP column call is identical for all samples (eg. the first row shows A/C for 47 samples and no call for 1 samples).

Index    Name    Chr    Position    ChiTest100    Het Excess    AA Freq    AB Freq    SNP    # Calls    # no calls
1    rs1000000    12    126890980    0.1542841    -0.1424561    0.06382979    0.2765957    [T/C]    47    1
2    rs1000002    3    183635768    0.5383009    0.06153843    0.173913    0.5217391    [A/G]    46    2
3    rs10000023    4    95733906    0.01898151    0.2345894    0.2708333    0.6041667    [T/G]    48    0
4    rs1000003    3    98342907    0.7411658    -0.03303099    0.6521739    0.3043478    [T/C]    46    2
5    rs10000030    4    103374154    0.09985247    0.1645569    0    0.2826087    [T/C]    46    2
6    rs10000037    4    38924330    0.916167    -0.01052631    0.04255319    0.3191489    [T/C]    47    1
7    rs10000041    4    165621955    0.079385    -0.1754266    0.680851    0.2553191    [A/C]    47    1
8    rs10000042    4    5237152    0.1619052    -0.1398692    0.0212766    0.1489362    [A/G]    47    1
9    rs10000049    4    118948220    0.1543059    -0.1424486    0.6595744    0.2765957    [A/C]    47    1
10    rs1000007    2    237752054    0.9848608    0.001897526    0.4166667    0.4583333    [A/G]    48    0
11    rs10000073    4    43022222    0.8291233    0.02158262    0.9375    0.0625    [A/G]    48    0
12    rs10000081    4    17348363    0.06784118    -0.182606    0.5744681    0.3191489    [T/C]    47    1

Thanks

[Neilfws]

This is not a very clear question, but it sounds like a "user error" in there somewhere.

[Darked89]

You can edit your question instead of spreading the question over several answers. Also please to use Code Sample format (see icon 101..) in the editor to show the data. Otherwise it is unreadable.

[David Quigley]

I put the data into the question and marked the demis001's answer for deletion.