tutorials:population-diversity:snp-chips
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tutorials:population-diversity:snp-chips [2020/09/22 10:09] – [Data analysis workflow with Plink 1.9] bngina | tutorials:population-diversity:snp-chips [2020/09/22 10:21] (current) – [Data analysis workflow with Plink 1.9] bngina | ||
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- | We can generate a file with filters added for the rate missing data in individuals '' | + | We can generate a file with filters added for the rate missing data in individuals '' |
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+ | The thresholds for these filters should be adjusted accordingly to the different data sets. | ||
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+ | < | ||
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+ | #### filter data ### | ||
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+ | plink --file ${file} \ | ||
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+ | --maf 0.01\ #SNPs with less than 1% minor allele frequencies | ||
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+ | --out ${out}/ | ||
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+ | </ | ||
===== Data analysis workflow with R and adegenet ===== | ===== Data analysis workflow with R and adegenet ===== | ||
tutorials/population-diversity/snp-chips.txt · Last modified: 2020/09/22 10:21 by bngina