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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 [2026/07/14 06:11] (current) – external edit 127.0.0.1
@@ Line 235: / Line 235: @@
 </code>
-We can generate a file with filters added for the rate missing data in individuals ''--mind'' and call rate for the SNPs ''--geno'' and also for the minor allele frequency //(MAF)// .
+We can generate a file with filters added for the rate missing data in individuals ''--mind'' and call rate for the SNPs ''--geno'' and also for the minor allele frequency //(MAF)// , with flag ''--maf''.
+The thresholds for these filters should be adjusted accordingly to the different data sets.
+<code>
+#### filter data ###
+plink --file ${file} \
+ --geno 0.05 \   #95% call rate of SNPs
+ --maf 0.01\     #SNPs with less than 1% minor allele frequencies
+ --mind 0.25 \   #individuals with more than 25% missing data
+ --out ${out}/bin_caprin_60k_fltrd \
+ --make-bed
+</code>
 ===== Data analysis workflow with R and adegenet =====