diff --git a/tools/human_genome_variation/sift.xml b/tools/human_genome_variation/sift.xml
index 443919e87fc..5c4f34e8104 100644
--- a/tools/human_genome_variation/sift.xml
+++ b/tools/human_genome_variation/sift.xml
@@ -2,7 +2,7 @@
   <description>predictions of functional sites</description>
 
   <command interpreter="bash">
-    sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$output_opts"
+    sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$comment_source.comment_col" "$output_opts"
   </command>
 
   <inputs>
@@ -13,12 +13,12 @@
     <param name="chrom_col"  type="data_column" data_ref="input" label="Column with chromosome"/>
     <param name="pos_col"    type="data_column" data_ref="input" numerical="true" label="Column with position"/>
     <param name="base" type="select" label="Position coordinates are">
-      <option value="0">zero-based</option>
       <option value="1" selected="true">one-based</option>
+      <option value="0">zero-based</option>
     </param>
     <param name="allele_col" type="data_column" data_ref="input" label="Column with allele"/>
     <conditional name="strand_source">
-      <param name="choice" type="select" label="Strand info">
+      <param name="strand_choice" type="select" label="Strand info">
         <option value="data_column" selected="true">a column in the dataset</option>
         <option value="all_pos">all on sense/forward/+ strand</option>
         <option value="all_neg">all on antisense/reverse/- strand</option>
@@ -33,6 +33,18 @@
         <param name="strand_col" type="hidden" value="-"/>
       </when>
     </conditional>
+    <conditional name="comment_source">
+      <param name="comment_choice" type="select" label="Include comment column">
+        <option value="no" selected="true">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="no">
+        <param name="comment_col" type="hidden" value="-"/>
+      </when>
+      <when value="yes">
+        <param name="comment_col" type="data_column" data_ref="input" label="Column with comment"/>
+      </when>
+    </conditional>
     <param name="output_opts" type="select" multiple="true" display="checkboxes" label="Include the following additional fields in the output">
       <option value="A">Ensembl Gene ID</option>
       <option value="B">Gene Name</option>
@@ -66,7 +78,7 @@
       <param name="pos_col" value="3"/>
       <param name="base" value="1"/>
       <param name="allele_col" value="5"/>
-      <param name="choice" value="data_column"/>
+      <param name="strand_choice" value="data_column"/>
       <param name="strand_col" value="4"/>
       <param name="output_opts" value="A"/>
       <output name="output" file="sift_variants_result.tab"/>
diff --git a/tools/human_genome_variation/sift_variants_wrapper.sh b/tools/human_genome_variation/sift_variants_wrapper.sh
index 67468c0a590..316dee75d2f 100755
--- a/tools/human_genome_variation/sift_variants_wrapper.sh
+++ b/tools/human_genome_variation/sift_variants_wrapper.sh
@@ -9,7 +9,8 @@ pos_col=$6
 base=$7
 allele_col=$8
 strand_col=$9
-output_opts=${10}
+comment_col=${10}
+output_opts=${11}
 
 working_dir=$PWD
 sift_input="$working_dir/sift_input.txt"
@@ -59,13 +60,23 @@ else
     strand_cvt='if ( '"${strand}"' == "+") { '"${strand}"' = "1" } else if ( '"${strand}"' == "-") { '"${strand}"' = "-1"}'
 fi
 
+if [ "$comment_col" = "-" ]; then
+    is_comment=0
+else
+    is_comment=1
+fi
+
 awk '
 BEGIN {FS="\t";OFS=","}
 {
     $'"${chrom_col}"' = tolower($'"${chrom_col}"')
     sub(/^chr/, "", $'"${chrom_col}"')
     '"${strand_cvt}"'
-    print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'
+    if ('"${is_comment}"') {
+      print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"', $'"${comment_col}"'
+    } else {
+      print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'
+    }
 }
 ' "$input_file" > "$sift_input"