find all snps/indels
 

is there a good way to find all the snps and indels (or just deletions in the read) from a sam file? has anyone written an MD tag parser that can do this? i tried a workaround by using the samtools variant caller, but that filters a lot of the snps out from my sam file -- i can't get it to output every single snp and indel. any ideas?

samtools and GATK, as just two examples, will parse .bam files, and output variants.

but they seem to filter variants. how do i completely turn the filter off and output every single variant present in the sam file?