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can I use GATK to analyze the drosophila Illumina sequence?

can I use GATK to analyze the drosophila Illumina sequence?
what should I pay attention to if I use GATK to do the drosophila genome sequence?

thanks

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yes you can. You will need to make sure you have the necessary input files (properly formatted reference, known variant sites etc) since we only provide these for human genomes. Apart from that the principles are essentially the same. I recommend you read through our documentation carefully before starting; see this link for introductory materials: http://www.broadinstitute.org/gatk/guide/topic?name=intro

  • BlueBlue Member

    Just to empirically concur, I've used some of the GATK tools successfully on Drosophila HiSeq whole-genome data.

    If using the Unified Genotyper, the expected heterozygosity option could be calibrated to e.g. 0.14 for D.melanogaster. I assume that this makes UG more sensitive to detect SNPs, which will be at a higher density in such organisms.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for chiming in, @Blue. You are correct about the purpose of the heterozygosity parameter.

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