Needs recommendation - Variant Call from RNA seq data of tumor-normal pairs.

Question

[field654]

Dear folks,

I understand that the WGS and WES are more frequently applied for variant call analysis.

I've seen a few reports using RNA-seq for variant calling. However, I didn't yet found one that support the tumor-normal sample pairs. Could anyone help recommend one?

Thank you.

Field

[cpad0112]

i am not sure if RNAseq is meant for that. GATK workflow for calling variants on RNASEQ data is available on internet, but it is not optimized. you can follow this old tutorial for starting: https://ssvbio.github.io/rna-seq-and-gatk-best-practices

[field654]

Hi Cpad, Thank you so much for your kind recommendation. I regularly use GATK for paired Tumor-Normal WES samples. It seems to me they haven't developed a paired Tumor-Normal set mode for RNA-seq.

I totally understand RNA-seq is not the best source for variant calling. I have to optimize the pipeline with my limited fund, unfortunately.

Best, Field

Answer 1

[grant.hovhannisyan]

Hi, indeed there are no gold-standard pipelines for SNP calling for RNA-Seq, so I would just recommend you to process your data with any popular software and then apply some stringent filters. For example, you can see how we performed SNP calling on FFPE paired cancer samples using bcftools, then filtering for quality of SNPs. In the end we got quite sensical results, so I think you can go ahead and try. https://www.mdpi.com/2072-6694/12/10/2844/htm

[field654]

Thank you so much for you recommendation. I would look deeper into your publication.

Best. Field