You're going to have to be way more specific about what you're trying to do. Every variant caller has to have some filters/assumptions, otherwise it would simply return every position in the genome (for perfect sensitivity and awful specificity!). That said, you can often relax the parameters on your variant caller of choice to provide additional low-confidence calls. In an extreme case, you could just run mpileup or bam-readcount on the entire genome saying "give me every single non-reference base and counts", but I suspect that wouldn't be particularly useful.

variant calling software typically allows to relax the filters as much as you want (FreeBayes - turn off ploidy assumption and tune the number of reads supporting the allele, VarScan2 is even more simple).