Merge pull request #34 from genxnetwork/hotfix/duplicates

1. Duplicated SNPs are removed properly
genxnetwork · Dec 1, 2021 · bb321fb · bb321fb
2 parents b50ad77 + 6e98cb1
commit bb321fb
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/rules/filter.smk b/rules/filter.smk
@@ -91,7 +91,7 @@ rule plink_clean_up:
         # remove dublicates
         cut -f 2 {params.input}.bim | sort | uniq -d > plink/snp.dups
         plink --bfile {params.input}          --exclude       plink/snp.dups                  --make-bed --out plink/merged_filter_dub   |& tee -a {log}
-        plink --bfile {params.input}          --extract       plink/merged_filter.bim.freq    --make-bed --out plink/merged_freq         |& tee -a {log}
+        plink --bfile plink/merged_filter_dub --extract       plink/merged_filter.bim.freq    --make-bed --out plink/merged_freq         |& tee -a {log}
         plink --bfile plink/merged_freq       --extract       plink/merged_filter.bim.chr     --make-bed --out plink/merged_extracted    |& tee -a {log}
         plink --bfile plink/merged_extracted  --flip          plink/merged_filter.bim.flip    --make-bed --out plink/merged_flipped      |& tee -a {log}
         plink --bfile plink/merged_flipped    --update-chr    plink/merged_filter.bim.chr     --make-bed --out plink/merged_chroped      |& tee -a {log}