How to run VCFTools and other variant callers on a set of .sam output of BBMap and other aligners?

Question

[elvissober]

How to run VCFTools and other variant callers on .sam outputs of BBMap and other aligners? Need a clear example in Unix shell and from Python subprocess and Java/Ruby, please. Thank you.

Answer 1

[Devon Ryan]

1. VCFtools doesn't call variants
2. Each caller gives example on its page. You will more or less never find examples from within python/java/ruby. Once you know what to type at the command line those will be obvious.
3. You want to use a sorted BAM file, not a SAM file.