GATK CNV Caller - issue with PostprocessGermlineCNVCalls
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8 days ago

Hi there,

I'm running gatk PostprocessGermlineCNVCalls for a cohort of hg19 aligned WES samples. I'm following the suggested pipeline here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants#5

However, in the final step when I try to process CNV calls for an individual sample, I get the following error, asking me to run FilterIntervals, but I've already run that earlier in the pipeline as suggested. Any suggestions on what's going on here? I'm using version GATK 4.2.

"java.lang.IllegalArgumentException: Records contain a singleton interval on contig (GL000228.1). Please run FilterIntervals tool first."

thanks!

PostprocessGermlineCNVCalls CNV GATK • 190 views
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That post was solved by updating GATK version, but I'm using an up-to-date version. Not sure what the solution could be here?

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it looks like gatk doesn't like when there is only one intervanl for one chromosome.

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