Tools used to handling output from MUMmer aligner You may want to read Wiki.
- MUMmerSNP2VCF.pl : recode SNPs/inDels in MUMmer output file to VCF format
MUMmerSNP2VCF.pl
Usage: perl MUMmerSNP2VCF.pl [queryID] [ref.sizes] [MUMmeroutput] queryID: ID used in the output VCF file, just used as the column name ref.size: tow column deliminated file, first column denote the chromosome, second is the size of it MUMmeroutput: output from MUMmer show-snp -Clr -x1 , remmember -x1