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Variant recalibration in Ion proton sequencing

lalirlalir CanadaMember

Hello,
I am beginning an exome sequencing project and so far, after conducing post-sequencing quality control, I see that my on-target bases (% of all bases covered by reads) are very high (>90%) so I think the variants called are quite specific. I should note that I used the Ion proton system for sequencing and this approach has an integrated variant caller, so I already have my VCF files. Due to the high on-target bases, I believe that the variants called should be quite specific and not very sensitive. Would you recommend I still run variant re-calibration to filter down to higher quality variants?

Answers

  • pdexheimerpdexheimer Member ✭✭✭✭

    I'll leave the specific recommendations to others, but I'll note that there's an enormous difference between the specificity of genomic capture and the specificity (or sensitivity) of variant calling.

  • lalirlalir CanadaMember

    Thank you, Yes, I suppose that the specificy/sensitivity is dependent on the variant caller used. It's called variant caller 4.2 and is integrated into the Ion proton system.

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