diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json
index c498464e..c8b03a96 100644
--- a/data/vtlib/final_output_prep.json
+++ b/data/vtlib/final_output_prep.json
@@ -123,7 +123,7 @@
 		}
 	},
 	{
-		"id":"crai_file",
+		"id":"cram_index_file",
 		"subst_constructor":{
 			"vals":[ {"subst":"outdatadir"}, "/", {"subst":"fopid"}, {"subst":"cram_idx_ext"} ],
 			"postproc":{"op":"concat", "pad":""}
@@ -368,7 +368,12 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":[ "cram_index", "-", {"subst":"crai_file"} ]
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "index",
+			{"subst":"cram_index_extra_flags", "required":false},
+			{"port":"cram", "direction":"in"},
+			{"port":"idx", "direction":"out"}
+		]
 	},
 	{
 		"id":"cram_seqchksum",
@@ -469,6 +474,7 @@
 	{ "id":"bam_file", "type":"RAFILE", "name":{"subst":"bam_file"} },
 	{ "id":"bam_index_file", "type":"OUTFILE", "name":{"subst":"bam_index_file"} },
 	{ "id":"cram_file", "type":"OUTFILE", "name":{"subst":"cram_file"} },
+	{ "id":"cram_index_file", "type":"OUTFILE", "name":{"subst":"cram_index_file"} },
 	{ "id":"bam_md5", "type":"OUTFILE", "name":{"subst":"bam_md5"} },
 	{ "id":"cram_md5", "type":"OUTFILE", "name":{"subst":"cram_md5"} },
 	{ "id":"seqchksum_file", "type":"RAFILE", "name":{"subst":"seqchksum_file"} },
@@ -517,7 +523,8 @@
 		}
 	},
 	{ "id":"cram_tee_to_md5", "from":"cram_tee:md5", "to":"create_cram_md5" },
-	{ "id":"cram_tee_to_crai", "from":"cram_tee:crai", "to":"cram_index" },
+	{ "id":"bam_to_idx", "from":"cram_tee:crai", "to":"cram_index:cram" },
+	{ "id":"idx_to_file", "from":"cram_index:idx", "to":"cram_index_file" },
 	{ "id":"cram_tee_to_bscs", "from":"cram_tee:seqchksum", "to":"cram_seqchksum" },
 	{ "id":"md5_to_postprocess", "from":"create_cram_md5", "to":"postprocess_md5" },
 	{ "id":"bmdmw_to_sts_F0x900", "from":"bmd_multiway:samtools_stats_F0x900", "to":"samtools_stats_F0x900" },