tutorials:population-diversity:snp-chips
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
tutorials:population-diversity:snp-chips [2020/09/22 09:17] – [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 | ||
---|---|---|---|
Line 235: | Line 235: | ||
</ | </ | ||
+ | We can generate a file with filters added for the rate missing data in individuals '' | ||
+ | |||
+ | The thresholds for these filters should be adjusted accordingly to the different data sets. | ||
+ | |||
+ | < | ||
+ | |||
+ | #### filter data ### | ||
+ | |||
+ | plink --file ${file} \ | ||
+ | | ||
+ | --maf 0.01\ #SNPs with less than 1% minor allele frequencies | ||
+ | | ||
+ | --out ${out}/ | ||
+ | | ||
+ | |||
+ | </ | ||
===== Data analysis workflow with R and adegenet ===== | ===== Data analysis workflow with R and adegenet ===== | ||
tutorials/population-diversity/snp-chips.1600766269.txt.gz · Last modified: 2020/09/22 09:17 by bngina