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Simulating reads to test methods

evolvedmicrobeevolvedmicrobe MGHMember Posts: 20
edited January 2013 in Ask the GATK team

I just wrote a walker to look for particular types of low frequency mutations, and I wanted to verify that the methods were working. I was hoping to simulate some illumina data with the variants and then run the methods against this data.

However, I don't know what a realistic error model is for common Illumina data and so am not sure how realistic my simulations are (Proportion of gaps, A->C versus A->G, etc.). Does the GATK include a read simulator? I saw one walker in the documentation but it seemed to rely on inputting settings that I didn't know about it and looked a bit out of date.

Any help appreciated.

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,390 admin
    edited January 2013

    We don't normally work with simulated data, so we don't have any up-to-date tools to do this, sorry. Perhaps someone in the community can suggest a good package that does this?

    EDIT: I stand corrected. See Mark's remark for pointers, although this only applies to folks within Broad. Suggestions from the community are still welcome to help external folks!

    Geraldine Van der Auwera, PhD

  • evolvedmicrobeevolvedmicrobe MGHMember Posts: 20

    Found a program that accounts for the error model (if in a somewhat unspecified way)...
    http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

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