SNP or Variant Calling and Annotation with RNA-seq Reads

Question

[vireen105]

What tools, algorithms or programs can I use to call variants given aligned RNA-seq reads or raw RNA-seq reads and connect those variants to their respective genes? And how does variant calling account for base call differences between reads?

Answer 1

[Pierre Lindenbaum]

https://nf-co.re/rnavar/1.0.0/

nf-core/rnavar is a bioinformatics best-practice analysis pipeline for GATK4 RNA variant calling.

Answer 2

[dthorbur]

GATK is one of the more used tools for variant calling both with DNA and RNA reads. Here is the pipeline they published recently.

And how does variant calling account for base call differences between reads?

I'm not sure I understand exactly what your question is after here. Can you elaborate? Given the ploidy of an organism, you may observe many different alleles for a given transcript and this is normal. GATK will emit confidences and depth, among other metrics for each variant.