replicate analyses and divide snp subsetsin admixture
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3.2 years ago
Daier ▴ 20

How can I use the admixture command to divide a large number of SNPs into subsets? For example, 50K SNPs are divided into 50 subsets, and each subset has 1K SNPs. After dividing the subsets, I choose the best K value and run all SNPs according to the best K value. How can I change the following commands?

If I want to replicate and run 10 times, what flag should I add to run?

for K in $(seq 1 15); do admixture --cv data.pruned.bed $K -j10 | tee log${K}.out; done grep -h CV log*.out

admixture subsets replicate • 415 views
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