--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse2/convertMAF.sh	Wed Jan 03 01:36:39 2024 +0000
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
+#  MAF file must contain the species name and chromosome name
+#  e.g. hg38.chr1 in the sequence identifiers.
+perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
+bgzip $4.sorted.bed
+tabix -p bed $4.sorted.bed.gz