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AritificialHaplotypeRG Mutect2

Hello,

I found an interesting variant call which are supported by 'ArtificialHaplotypeRG' (total 8 reads) when using Mutect2.
They don't seem to be real reads.
What are the reads ?
Is the call reliable?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ensel
    Hi,

    Those are not actual reads supporting the alleles, they are "artificial haplotypes" constructed by HaplotypeCaller during the local reassembly step. Have a look at this document for more information.

    -Sheila

  • enselensel Member

    Hello, Sheila

    Thank you for your helps always!

    Could you check another discussion that I raised ?

    'ReadBackedPhasing missed calls '

  • enselensel Member

    Hello,
    So, 'the artificial haplotype RG' are made up reads which are not present in the input bam file.
    Are the artifical haplotype reads excluded in variant calling ?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ensel
    Hi,

    Yes, the artificial haplotypes are not used in variant calling. They are simply made as part of the haplotype creation step. You can read more about it in the Methods and Algorithms section.

    -Sheila

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