SVM based VCF filter

Question

[manojkumarbioinfo]

Hi,

I would like to know is there any free SVM based tools for filtering my VCF file. if its there kindly me tell me.

[Devon Ryan]

An SVM-based tool for filtering VCF files? What exactly are you trying to accomplish?

[manojkumarbioinfo]

@Devon Ryan Yes that what i need

[manojkumarbioinfo]

i just wanted to filter out my variants based on true positive and false positive. i have a separate data of true positive one . now i want to filter out my variants.@DevonRyan

Answer 1

[Mike]

You can try GATK's VQSR package. Variant Quality Score Recalibration (VQSR)