How to get all variants in original BAM file with HaplotypeCaller? (No correction and BAMout)

Question

[Clark_BioMorgan]

Dear All,

As you know when we use HaplotypeCaller in the variant calling pipeline, the script makes corrections and focuses on the true positive variants. and eliminates many vairant so called wrong one or caused by the artifact sequencing. But no matter what I would like to get all the variants comes directly from the original BAM file. How should I use HaplotypeCaller so that my original BAM and the final BAMout have exactly the same variants?

Thanks in advance.

[Devon Ryan]

If you want that then why not use samtools mpileup or something like that instead? If you don't want to output likely variants but all differences then don't use a variant caller.