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I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (here) and Maftools (here). I don't know which method is better, or are there any other better tools you would recommend?

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    $\begingroup$ MAFtools is not a variant calling tool. Google "benchmark somatic variant callers" and read some papers - MuTect2, SomaticSniper, VarScan2, Strelka etc are some relevant tools. $\endgroup$
    – Ram RS
    Commented Mar 28, 2022 at 18:36
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    $\begingroup$ What organism are you working on, i.e. your sample? This has an enormous impact on the approach and the tools. $\endgroup$
    – M__
    Commented Mar 29, 2022 at 3:10

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