Mutect2 variant calling without a known intervals list

EleniStylianou · October 2018

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.

bhanuGandham · October 2018

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.

Regards
Bhanu

Angry_Panda · August 2019

Hi @bhanuGandham , I am doing the similar thing. I used broad institute github page offered testing material ,wdl and json files. mainly tested mutect2.wdl and mutect2-normal-normal.wdl, locally. But I dont know how to modify the interval_list file download from google bucket. should I replace "UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta" to "/local path/Homo_sapiens_assembly19.fasta" ? or could I run the analysis without indicating intervals?

bhanuGandham · August 2019

HI @Angry_Panda

Lets use one thread for this question. Working on this question in this thread: https://gatkforums.broadinstitute.org/gatk/discussion/24295/how-to-modify-whole-exome-agilent-1-1-refseq-plus-3-boosters-homo-sapiens-assembly19-baits-interval#latest

Mutect2 variant calling without a known intervals list

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