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meyer-lab-cshl / plinkQC

R package for quality control of plink genetic datasets
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plinkQC a single sample #41

Closed jielab closed 3 years ago

jielab commented 3 years ago

Hi, I am working individual 23&Me data, so each dataset has only one sample, for example, the genotype data for myself.

In this case, I also want to get a QC report, to see how many SNPs in total, how many of those are missing, what their frequency is like in a reference such as 1000G.

Is there a way to do this? Right now, plinkQC seems to work on a plink file with lots of samples.

Thank you & best regards, jie

HannahVMeyer commented 3 years ago

Hi Jie, I would combine them into one dataset first using the plink —merge-list command on the command line. You can then use plinkQC as described in the vignettes.

On 8 Feb 2021, at 20:08, Jie Huang notifications@github.com wrote:

 Hi, I am working individual 23&Me data, so each dataset has only one sample, for example, the genotype data for myself.

In this case, I also want to get a QC report, to see how many SNPs in total, how many of those are missing, what their frequency is like in a reference such as 1000G.

Is there a way to do this? Right now, plinkQC seems to work on a plink file with lots of samples.

Thank you & best regards, jie

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jielab commented 3 years ago

But I just need to run QC for a sample, for my own 23&Me file with about 1M SNPs. Can you please let me know if there is a tool to do this?

Thanks! Jie

HannahVMeyer commented 3 years ago

I see. plinkQC is not the right tool for you then. You can’t compute frequencies from a single sample, you’ll need something to compare to. And that’s a different type of analysis. Good luck with your analysis!

On 8 Feb 2021, at 21:51, Jie Huang notifications@github.com wrote:

 But I just need to run QC for a sample, for my own 23&Me file with about 1M SNPs. Can you please let me know if there is a tool to do this?

Thanks! Jie

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