It's not really possible to convert bam
to vcf
. bam
is a mapping file, it does not contain the information about variants, this information needs to be inferred in process called variant calling. I find important to mention that it's not just a different format of the same thing.
How to call variants (a vcf
file) from mapped reads (a bam
file) is very broad question, it depends on the sequencing technology (Illumina, PacBio, ...), the type of sequencing (whole genome sequencing, RAD, RNA-seq, ...), the sampling (calling of individuals vs population variability), the quality of a reference (human vs denovo assembly made by a postdoc in your lab)... For a lot of cases the answer is simply GATK, partially because it has well written manual, but mainly just because many people use it.
Some more detailed cases are well answered in more specific questions :