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shishuo16 / RefRGim

an intelligent genotype imputation reference recommendation method with convolutional neural networks
BSD 3-Clause "New" or "Revised" License
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what is SNP.info.bz2 #1

Open chantisakee opened 2 years ago

chantisakee commented 2 years ago

RefRGim is so interesting and i would like to impute my data which is based on Hg38. So I have to adjust some code and prepare files. I wonder how to get SNP.info.bz2 for hg38? Could you please tell me more about SNP.info.bz2 especially in the last column?

Thank you so much

shishuo16 commented 2 years ago

Hi, the SNP.info.bz2 file contains the SNP (chr, pos, ref, alt) we used in the model and the prefix of pre-trained network model that contained the SNP. RefRGim needs the exact SNPs (chr, pos, ref, alt) to work, as it was trained with those SNPs.

chantisakee commented 2 years ago

Thanks for the response! :)

i'm just wondering if i want to add more samples in 1000G. What data do i have to prepare and how? Do you have any instruction? According to the paper, there are raw code for the training .. I found that there are test.sample_snp.matrix.bz2 and test.sample_population.matrix anything else I have to prepare?

Thank you every much. I do really appreciate your work.