Package to predict genomic variants from rna-seq read data

Question

[dk0319]

While performing RNA-seq analysis I noticed that manually observing the mapped reads with a genome viewer can accurately describe known genomic mutations such as SNV's and deletions. I was interested if anyone knows of existing packages that can predict genomic variants from the RNA-seq reads?

[GenoMax]

From GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels-

Please see the discussion in this thread as you contemplate calling variants from RNAseq data: Inferring genotype based on RNA sequences (RNA-seq variant calling)

Answer 1

[ATpoint]

Rna-Seq Data Variant Calling

... and many other threads, please use google and the search function.

By the way, I would not say that visual inspection "accurately" describes any variant. Base and alignment and multiple heuristics such as relative position of the variant in the read, presence of homopolymers etc need to be taken into account, all the things variant callers do under the hood.

[dk0319]

Thanks, I should have emphasized the "known" aspect