RNAseq short variant discovery (SNPs + Indels)
In the RNAseq short variant discovery (SNPs + Indels) pipeline HaplotypeCaller is mentioned for variant calling.
I am using somatic data (RNA seq Data) of cancer patient for variant calling.
Should I use Haplotype Caller or Mutect2 ?
Thanks and Regards
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Hi Jay Singh,
I have the some question. Did you figure out which variant caller to use for somatic RNAseq data, HaplotypeCaller or Mutect2?
The current pipeline for RNA-seq variant discovery is focused on germline variants, which is why HaplotypeCaller is recommended. However, Mutect2 may be the correct choice when analyzing somatic variants. Here is a link to a discussion post about Mutect2 for RNA-seq with some suggestions and considerations from one of the GATK developers: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056152451-Mutect2-for-RNA-seq- There isn't currently a best practices for somatic RNA-seq but I hope you find this helpful.
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