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recommendation on UnifiedGenotyper inputs for SOLiD data

We are trying to call variants from SOLiD data using the Unified Genotyper. Do you have recommendations on the -stand_call_conf and -stand_emit_conf with SOLiD data?

Thanks

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    We don't have any specific recommendations for using the UG on SOLiD data, as we don't use that data type much ourselves. I would recommend using fairly low thresholds, then focusing on variant recalibration to filter the resulting calls. You may need to experiment a little to find the settings that make sense for your project. Good luck!

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