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tutorials:population-diversity:snp-chips

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tutorials:population-diversity:snp-chips [2020/09/22 10:09]
bngina [Data analysis workflow with Plink 1.9]
tutorials:population-diversity:snp-chips [2020/09/22 10:21] (current)
bngina [Data analysis workflow with Plink 1.9]
Line 235: Line 235:
 </code> </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 ===== ===== Data analysis workflow with R and adegenet =====
  
tutorials/population-diversity/snp-chips.txt · Last modified: 2020/09/22 10:21 by bngina