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!