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Calling Variants with more than one tool necessary?

sp580sp580 GermanyMember

Hello!

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!

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