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Old 12-14-2018, 05:56 PM   #1
ibrakurt
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Location: Boston

Join Date: Dec 2018
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Post Trio SNP data to test script (preferably from Infinium Global Screening Array)

Hello all,

I want to write my own simple script to test whether I can QC a child's SNP data by checking his/her parents' SNP data. Obviously my expectation is to get an output of ~50% from mother, and ~50% father. To be able to test this script, I am looking for sample trio SNP data, preferably from Illumina Infinium GSA array in the following format:

Code:
SNP Name    Sample ID   GC Score    Allele1 - Forward   Allele2 - Forward   Chr Position    B Allele Freq   Log R Ratio
GSA-rs10048794  sample1 0.9301  C   C   2   14825598    0.9891  0.077
GSA-rs1004889   sample1 0.9394  G   G   12  83516749    1   0.0237
Do you guys have any idea where I can find such data? It does not have to be GSA array, however it would be great if all 3 person's SNP data format are matching, as it is tough for my level to dive into all different SNP data formats and normalize them to each other.

Lastly, do you guys know of a script that already would take 3 SNP data input and tell the relationship among the 3, such as trio?

Note: I am someone with weak bioinformatics background.

Thanks a lot!
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