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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

disable NotPrimaryAlignmentFilter in DepthOfCoverage

Can someone point me to documentation on how I can run DepthOfCoverage without the NotPrimaryAlignmentFilter?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    It's not possible to disable filters that are on by default, sorry.

  • "It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative[...]"

    I disagree:
    This filter removes reads sequenced from the repeat regions, where reads shall map as many times as there are repeated region.
    This is their rightful place. This filter won't allow us to deal with repeat regions (with the depth of coverage).
    May be it can be very useful, in that case, to add a small function to allow us to disable default filter.

    Regards,

    Rémi

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @remimaglione
    Hi Rémi,

    I see what you are saying, but Depth of Coverage should give the coverage that can be used at a site. If you disable the filters, you will get inaccurate coverage at sites where the reads will be filtered out in other downstream tools.

    -Sheila

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