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what interval files do you guys use for human exome variant calling?

I downloaded my intervals files from UCSC human exome captured file (hg19_exome_sorted.bed), but I keep getting lots of "./." in the final VCF files. I asked before in this forum, and I remember Geraldine said this may be because of sub-optimal interval files. This made me wonder what you guys use for human exome variant calling?


  • pdexheimerpdexheimer Member ✭✭✭✭

    The right one :)

    There are at least 10 or 15 catalog exome enrichment kits from three vendors, each one with different coverage regions - to say nothing of the custom kits out there. Call the lab and find out which one they used

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    You get "./." at sites where there is no useable coverage. If you're using an intervals file that does not match the actual exome targets used to generate your data, it is possible you're asking the program to call variants on intervals that have no data at all (and you may be omitting intervals where you do have data). Ideally you should check exactly which targets were used for your data. The major sequencing vendors all provide intervals lists that match their kits. FYI, we (at Broad) use a custom-designed exome capture targets list; I believe the file is in the bundle, but it may not be what you need.

  • rcholicrcholic DenverMember

    @Geraldine & @pdexheimer: Thanks for the replies.

    I just heard back from the lab people I work with. They told me the exome-enrichment kit used is:
    Agilent Exome Capture Kit Sure Select XT Target Enrichment System for Illumina Paired –End Sequencing Library. Version XTV4

    Do you have a recommendation for what interval list I should use for this kit? or this question would be better directed to Agilent? Thanks for helping.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah, that's a fairly classic one -- you can get the file directly from Agilent's website, I believe. You may need to register on their website to access it.

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