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.
Calling Variants with more than one tool necessary?
I am currently executing GATK's best practices pipeline. However, I am trying to decide if thereafter I should call variants using other tools, as it is suggested in this 2017's review.
I am working with mouse data (60 samples, ~20x coverage per sample) and most papers use one variant calling tool (GATK or SAM/BCFtools), except for two studies using 3 callers (GATK, SAM/BCFtools, QCALL), but they are relatively "old" (2011 & 2012).
I am looking for some help to make up my mind between the choices:
- Only GATK
- GATK plus SAM/BCFtools
- GATK plus SAM/BCFtools plust Tool3
Since I have only three weeks to finish this part of the project, this decission is critical.
Looking forwards for your suggestions!