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6.5 years ago
MatthewP
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1.4k
Hello, I am learning gatk somatic CNV pipeline following this tutorial. The gatk command CollectAllelicCounts needs one interval_list for -L parameter.
My question is how to construct such interval file for WES?
If I use interval file containing whole region captured by my WES kit, the outcome file will be too big for next ModelSegments command.
Rather, you want to pass a list of sites of common variation in your exome target regions, which can be constructed using e.g. gnomAD.
I quoted this answer from gatk forum(link), however I need more detail about how to do the construction.
Thanks.