Hello,

my understanding of these two options is, that --min-coverage defines how many reads must be on that position before freebayes starts to look whether there are reads that doesn't support the reference. -C defines how many reads must support the non-reference base before checking more criterias.

So what you are looking for is -C. But unless I'm not absolutly sure what an option does, I wouldn't change the default parameters of a variant caller. Does freebayes do any filtering of reads before counting (MapQ, Duplicates,...)? How it does count overlapping paired reads? I don't know. A better way would be to do the variant calling with default parameters and filter your vcf afterwards. It contains the information how many read support the alternate allele.

fin swimmer