sort the decomposed VCF file

pangenome · Jan 23, 2024 · f581af3 · f581af3
1 parent 4dfa1cf
commit f581af3
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/pggb b/pggb
@@ -667,10 +667,9 @@ if [[ $vcf_spec != false ]]; then
             bgzip -c -@ $threads "$vcf" > "$vcf".gz
             TEMPDIR=$(pwd) $timer -f "$fmt" vcfbub -l 0 -a $pop_length --input "$vcf".gz | TEMPDIR=$(pwd) $timer -f "$fmt" vcfwave -I 1000 -t $threads > "$vcf_decomposed_tmp"
 
-            #TODO: to remove when vcfwave will be bug-free
-            # The TYPE info sometimes is wrong/missing
-            # There are variants without the ALT allele
-            bcftools annotate -x INFO/TYPE "$vcf_decomposed_tmp"  | awk '$5 != "."' > "$vcf_decomposed"
+            #TODO: remove "bcftools annotate" when vcfwave will be bug-free.
+            # The TYPE info sometimes is wrong/missing and there are variants without the ALT allele.
+            bcftools sort -T "$temp_dir" | bcftools annotate -x INFO/TYPE "$vcf_decomposed_tmp"  | awk '$5 != "."' > "$vcf_decomposed"
             rm "$vcf_decomposed_tmp" "$vcf".gz
 
             bcftools stats "$vcf_decomposed" > "$vcf_decomposed".stats