Variant calling on aligned BAM files of WES

Question

[atheeth14]

Could someone help in identifying SNVs in aligned BAM files alone? The index files provided are not .bai format. I know i need to use callVariants function, but the documentation is not clear on how to use this for WES. The exact code snippets would be better.

[GenoMax]

Creating a .bai index is as simple as samtools index your.bam.

[igor]

I know i need to use callVariants function

What tool is this function from?

The exact code snippets would be better

This applies to original question as well.