Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Variant calling on BAMS from different Alignment Tools

I have a question about performing variant calling on multiple BAM files that have been generated using 2 different alignment tools (for example - 'BWA-mem' and 'Novoalign' in my case).

For example - Total 4 Samples and one Bam per Sample. Sample 1 & 2 BAMs are from BWA-mem. Sample 3 & 4 BAMs are from Novoalign. And all 4 of these BAMs go through the usual best practices QC after alignment (Duplicate removal/BQSR etc.)

  1. Is it recommended to use HaplotypeCaller on Sample 1, 2, 3 & 4 together (either in gVCF mode or regular mode)? (Since their BAMs were generated using different alignment tools)
  2. If yes, any specific QC to perform pre-calling on BAMs (or post-calling on VCFs) to ensure the compatibility of BAMs with one another?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Shalabh,

    I have never tested this out myself, but I think there should not be an issue with calling variant on all 4 samples together. However, I would test both ways (4 vs 2 and 2) just to confirm there are indeed no major differences.


Sign In or Register to comment.