Sort and reformat permutation p-values

eQTL-Catalogue · Jul 2, 2020 · 6d60124 · 6d60124
1 parent 348e674
commit 6d60124
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -371,7 +371,8 @@ process merge_permutation_batches {
 
     script:
     """
-    cat ${batch_file_names.join(' ')} | bgzip > ${study_qtl_group}.permuted.txt.gz
+    cat ${batch_file_names.join(' ')} | csvtk space2tab | sort -k11n -k12n > merged.txt
+    cut -f 1,6,7,8,10,11,12,18,19,20,21 merged.txt | csvtk add-header -t -n molecular_trait_object_id,molecular_trait_id,n_traits,n_variants,variant,chromosome,position,pvalue,beta,p_perm,p_beta | bgzip > ${study_qtl_group}.permuted.txt.gz
     """
 }