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GATK for RNA seq variant calling

I am very new to this but I was just wondering what commands do people normally use with HaplotypeCaller for variant calling with GATK on RNA-seq data. I am trying to following the pipeline they have established here https://gatk.broadinstitute.org/hc/en-us/articles/360035531192?id=4067 but wasn't too sure of the best set of commands to use.

rna-seq snp variant calling
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written by danson.wooi • danson.wooi

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