SVM based Filtering For NGS data

Question

[manojkumarbioinfo]

Hi,

I would like to know is there any available Scripts or Tools based on Support Vector Machine (SVM) for filtering the variants from NGS data if there is any tool or code can you tell me.

Thanking you.

Answer 1

[Vivek]

As far as I'm aware, the only ML based software tool for variant filtering is the GATK's variant quality score recalibration and it uses a Gaussian mixture model.

http://gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr

[manojkumarbioinfo]

But VQSR is only used for identify the quality for the variants. but i want to have something different if you check the bcbio they are having a own pipeline where they use some SVM classifier for filtering the variants i need a tool like that the main thing is i dont want their full pipeline i just need the SVM for filtering the variants. https://bcbio.wordpress.com/tag/clinical/