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SNPs.txt
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###################STACKS SNP calling##################################################################
ref_map.pl -T 8 --samples DIRECTORYTOSORTEDBAMFILES --popmap ./SPECIES_popmap.txt -o OUTDIR -X "populations: --plink"
###################PLINK for quality filters###########################################################
##NOTE: use --recode flexibly for different output
####("--recode " to create .ped file for next step;
#####"--reocde vcf" to create .vcf file for R-based analyses;
#####"--recode12" to create .ped file for ADMIXTURE;
#####"--recode A" to create .raw file for R-based DAPC analysis)
##DATASET with 10% missingness (DATA1)
plink --file STACKSOUTPUT --allow-extra-chr --geno 0.1 --out DATA1 --recode
##DATASET with 10% missingness, linked loci filtered (DATA1L)
plink --file DATA1 --allow-extra-chr --allow-no-sex --indep-pairwise 25 10 0.95
plink --file DATA1 --extract plink.prune.in --allow-extra-chr --out DATA1L --recode
##DATASET with 10% missingness, loci with minimum allele frequency < 0.05 filtered (DATA15)
plink --file DATA1 --maf 0.05 --allow-extra-chr --out DATA15 --recode
##DATASET with 10% missingness, linked loci filtered, loci with minimum allele frequency < 0.05 filtered (DATA1L5)
plink --file DATA1L --maf 0.05 --allow-extra-chr --out DATA1L5 --recode
##DATASET with 0% missingness (DATA0)
plink --file STACKOUTPUT --allow-extra-chr --geno 0 --out DATA0 --recode
##DATASET with 0% missingness, linked loci filtered (DATA0L)
plink --file DATA0 --allow-extra-chr --allow-no-sex --indep-pairwise 25 10 0.95
plink --file DATA0 --extract plink.prune.in --allow-extra-chr --out DATA0L --recode
##DATASET with 0% missingness, loci with minimum allele frequency < 0.05 filtered (DATA05)
plink --file DATA0 --maf 0.05 --allow-extra-chr --out DATA05 --recode
##DATASET with 0% missingness, linked loci filtered, loci with minimum allele frequency < 0.05 filtered (DATA0L5)
plink --file DATA0L --maf 0.05 --allow-extra-chr --out DATA0L5 --recode