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Local reference for UG SNP-calling

BlueBlue Member Posts: 48
edited March 2013 in Ask the GATK team

The Unified Genotyper calls SNPs relative to the specified, publicly-available reference assembly.

How can I call SNPs (in many samples, with UG) relative to an in-house individual, which I have sequenced at high-coverage?

My current solution is to perform a de novo assembly on the in-house reference individual using e.g. Velvet, and then simply use the fasta as the reference for UG.

Can the publicly-available reference assembly still be useful here for speeding up the mapping and filling-in missing parts ?

My organism is Drosophila melanogaster.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,739 admin
    Answer ✓

    It sounds like you want to assemble your in house reference genome using the public reference genome as a scaffold rather than doing it entirely de novo.

    Genome assembly isn't our department so I can't advise you on this, but I'd recommend asking somewhere like SeqAnswers what is the best aligner to do this.

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,739 admin
    Answer ✓

    It sounds like you want to assemble your in house reference genome using the public reference genome as a scaffold rather than doing it entirely de novo.

    Genome assembly isn't our department so I can't advise you on this, but I'd recommend asking somewhere like SeqAnswers what is the best aligner to do this.

    Geraldine Van der Auwera, PhD

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