Determining bin size

[Anna Elisabeth Backhaus]

Hi,

I have been using BLINK to run GWAS on whole genome sequencing data and its working so well. However, I now want to analyse the QTN regions and I don't fully understand how to determine the size of the candidate region. For example, we have one very significant marker, how do I find the start and end of the candidate region, ie how do I find out the bin size? Do I need to run a different program to find what is in LD? Or does this output hold the information?

"

length_bin_min=4

LD_cutoff is 0.700000

Number of all the candidate QTNs is 4

indicator=0, q0=13

"

Does the bin_min hold this information?

Thank you so much for any help in advance!!

best,

Anna

[Meng Huang]

Hi Anna,

BLINK could only find out the significant associated SNPs. If you want to do other analysis after that, you may need to use different software. 

The length_bin_min means the number of possible QTNs in the model, not refer to the LD bin.

Thanks,

Meng

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[Anna Elisabeth Backhaus]

Thank you Meng, I will just use LDBlockSize to determine the full region. thanks again for the quick response!

I have one other question if that's okay: If I save PCA data as .cov file in the same folder the analysis does not start running (for BLINK-C). Is there any known reason for this or common mistake?

Best,

Anna

[Meng Huang]

BLINK-C could automatically read the .cov file in the current path, I guess the format of cov file may be wrong. 

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[Anna Elisabeth Backhaus]

Thanks Meng, I will work with the format!