Benchmarking pipeline for Variant identification using RNA-seq data

[ahkam.s]

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ahkam.s • 0

I have to benchmark the (germline and somatic) variant identification pipeline which uses RNA seq data alone without any matched-normal. I would like to know the reference dataset (and the pipeline on which the dataset was run) with known variants that help to validate the pipeline results. The reference dataset which I use should be comparable regardless of the dataset specific to certain disease. Thanks all in advance for your responses.

[Ben3]

Hello ahkam.s,

Could you give us a little bit more information about the data you are working with?

What organism is this from, what system have you used?

Any additional information about the pipeline?

Feel free to give as much detail as you can and that can help us pinpoint how to help you.

[ahkam.s]

Hi Ben3,
Thanks for the response. The samples I have are of humans, and for learning purpose, I thought of comparing with one of the open-source RNA-seq variant calling pipeline.