For my own necessity I have recently made this tool that, contrary to the original
mummer-2-vcf.pl script, converts the snps output of the
show-snps MUMmer tool to a real VCF file (with header and the like).
EDIT: please use the
--input-header option if your input
*.snps file has a header. Otherwise you will have an
IndexError somewhere in the code.
It worked with my data, and it should work with yours. Anyone interested in giving it a test run?