- " -r, --refseq <file.fa> The reference sequence, required when indels are present.\n",
- " -s, --snps-only Ignore indels.\n",
- " -t, --column-title <string> The column title.\n",
- " -h, -?, --help This help message.\n",
+ " -h, -?, --help This help message.\n",
+ " -i, --indels-only Ignore SNPs.\n",
+ " -r, --refseq <file.fa> The reference sequence, required when indels are present.\n",
+ " -R, --keep-ref Print reference alleles as well.\n",
+ " -s, --snps-only Ignore indels.\n",
+ " -t, --column-title <string> The column title.\n",