Ignoring indels when constructing haplotypes

Hello,

Is it possible to ignore indels when reconstructing haplotypes using haplotypcaller? If not, would setting --PCR-indel-model to hostile be the best way to downplay indels?

Best,
Elliott

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Elliott
    Hi Elliott,

    Why do you want to ignore indels?

    Along with your idea, you can also set a very low value for indelHeterozygosity.

    -Sheila

  • ElliottElliott Member
    edited January 2016

    Hi Sheila,

    Thanks very much for your comment.

    Some sequencing technologies like iontorrent produce very high of false positive rates for indels. My thinking is, a random scattering of false indels across reads which contain a true heterozygous SNV will produce a high number of haplotypes. This may result in the loss of informative reads that do not fit the most probable haplotypes because of these false indels. Perhaps my thinking here is wrong?

    Best,
    Elliott

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