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max_alt_alleles in UnifiedGenotyper

mike_boursnellmike_boursnell Posts: 85Member

If you are using UnifiedGenotyper to call Indels, and you are looking at an Indel which is hard to sequence (say 9 Ts versus 10 Ts) the sequencing may generate more different Indel alleles than there really are. What is the best way to deal with this situation if you actually only want one alt allele called? If you limit max_alt_alleles to 2, what does the software do?

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,781Administrator, GATK Dev admin

    If there are more alleles present in the data than the amount of alleles specified by max_alt_alleles, the UG will choose those that are the most likely and not emit the rest.

    FYI, the HaplotypeCaller is much better at making sense of indels, so unless you're working with ridiculously high numbers of samples that you have to call jointly, or with non-diploid genomes, you should try the HC and see if you get better results.

    Geraldine Van der Auwera, PhD

  • mike_boursnellmike_boursnell Posts: 85Member

    Thanks. Is HC recommended for the dog genome. Does it need HapMap data for example?

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