Mutect2 variant calling without a known intervals list

Hi Sheila,
I am analyzing somatic variants in exome sequencing data from paired tumor/normal samples for which the intervals list is unknown. I have been using hs38Dh.fa as the reference genome. In the absence of a known intervals list what should I do when performing Mutect2 variant calling? Should I use the wgs_calling_regions_hg38.interval_list?
Thank you very much.


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @EleniStylianou

    For exomes and similarly targeted data types, the interval list should correspond to the capture targets used for the library prep, and is typically provided by the prep kit manufacturer (with versions for each ref genome build of course).

    We make our exome interval lists available, but be aware that they are specific to the custom exome targeting kits used at the Broad. If you got your sequencing done somewhere else, you should seek to get the appropriate intervals list from the sequencing provider.


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