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!