Hello everyone,
I am in the process of building a pipeline for multisample variant calling and have some questions regarding tool usage and their safety. Specifically, I would like to discuss mapping and variant calling.
Mapping:
I have mapped my reads using BWA-MEME (not BWA-MEM) from this repository: BWA-MEME GitHub.
Variant Calling:
For variant calling, I am using GATK HaplotypeCaller with DRAGEN mode enabled. Afterward, I build a GenomicsDB and consolidate the GVCFs. I follow GATK's best practices, assuming that BWA-MEME produces similar outputs to BWA-MEM (BWA-MEM2). Here is the reference I use for the DRAGEN pipeline: GATK DRAGEN Mode Guide.
Questions:
- Do you have any opinions or experiences with these tools?
- Is it problematic to use DRAGEN mode? From my understanding, it performs better, at least before the merging (GATK-DRAGEN).
I found some literature that supports the use of these tools: Performance Evaluation of Variant Calling Tools.
I would greatly appreciate any insights or advice on this matter.
Thank you!! pipeline
I wonder if GATK+Dragen is always under active development ....
Haha, honestly, with all due respect to the GATK developers, it feels like GATK is always in some form of beta... and let's not even get started on Spark. Still, despite all the bugs and troubleshooting, I believe the GATK "suite" performs better in most cases.