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Post by jsealock on Oct 3, 2019 19:47:59 GMT
I was hoping to use fastGWA on biobank data on around 70k individuals. To create a GRM using --make-grm it would take 11 days to generate, so to cut down the time I wanted to use --make-grm-part. However, it's not clear to me how this flag affects the GRM calculation. Is the GRM still calculated pairwise across the entire sample or only pairwise within the part? For example, if I use 70 parts will the 1000 people in each part be compared to the other 69k or just the other 999 individuals in the same part? thanks!
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ax
New Member
Posts: 27
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Post by ax on Dec 6, 2019 1:56:41 GMT
Hi jsealock,
It still compares to other 69k individuals in your case.
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Post by elaine on Mar 5, 2022 19:37:58 GMT
Hi jsealock, It still compares to other 69k individuals in your case. Based on this question, I tried to convert grm.gz in plain text file for each part GRM. But it seems only 999*(999-1)/2 rows are output which means only output the GRM within each part instead of all other 69K individuals. I am confused about this point. Another question is if the grm.N.bin file only includes a number, why does the file size of test.grm.N.bin be the same with test.grm.bin? |
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