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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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Mutect2 variant calling without a known intervals list
EleniStylianou
Member ❠
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.
Answers
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
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?
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