VariantRecalibrator.

Hi,
I have bovine next generation sequence results from illumina miseq platform. In the data I have specific three genes. I need to do variantrecalibration, first what would I need to do this analysis? In the example command line, all the data sets origin is human since I am working with "nonhuman organism" I don't have every file on the list.
What information from the file would be essential for the VariantRecalibration step?

Also, I don't have the vcf file but one could be generated from the bovineHD SNP , so the generated file from bovineHD array manifest would be suitable to use for next generation sequence variantrecalibration analysis?

Thank you

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @bnuket , please have a look at the best practices recommendations, as well as the slides from the presentations posted earlier this week on the GATK blog. In particular there is one on dealing with non-human organisms that you will find useful.

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