Hi Guys,

I want to call variants for 36 samples having matched normal. Can you suggest me how to run (what are the steps) GATK in this case ? Previously, I used haplotype caller for pathological samples. But in case of matched samples (where we have normal info), mutect2 seems to be used (https://gatk.broadinstitute.org/hc/en-us/community/posts/360057810051-Mutect2-somatic-variant-calling-with-without-matched-normal-sample).

I am not confirm what path should I follow? I also posted my query to GATK (https://gatk.broadinstitute.org/hc/en-us/community/posts/4414698096795-Variant-calling-for-matched-samples).

Please give your suggestions.

Thanks and regards