diff --git a/src/modules/modkit.nf b/src/modules/modkit.nf
index 16b98bcaca90ab335048408a7ea7aaa8666a249f..d5a1a9da7165b85c6b8f7384be697ae5f4ab7625 100755
--- a/src/modules/modkit.nf
+++ b/src/modules/modkit.nf
@@ -13,7 +13,7 @@ process MODKIT {
         """
         echo "starting modkit"
         ## Make Methylation TSV file
-        modkit extract full --queue-size 1000 -t 4 -i 10000 --mapped-only "${bam}" "${id}_modkit_output.tsv"
+        modkit extract full --bgzf --queue-size 1000 -t 4 -i 10000 --mapped-only "${bam}" "${id}_modkit_output.tsv"
         echo "extract successful"
         ## Make Methylation Table
         modkit pileup -t 4 -i 10000 --chunk-size 4 "${bam}" "${id}_modkit_pileup.bed" --log-filepath "${id}_modkit_pileup.log"