Error in GATK germline CNV caller

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3.7 years ago

cocchi.e89 ▴ 260

I am trying to run GATK CNV germline on some human hg19 WGS samples. I followed the passages reported in their best-practice guidelines. I started with a 300 bp bin_length in PreProcessIntervals. But after all passages if I try to extract values from a single sample with PostprocessGermlineCNVCalls I got the same error for all samples:

java.lang.IllegalArgumentException: Records contain a singleton interval on contig (17). Please run FilterIntervals tool first.

The problem is that I already run FilterIntervals on the same cohort as recommended.

Does anybody ever had a similar problem?

Thank you very much in advance for any help

gatk cnv germline • 1.2k views

ADD COMMENT • link 3.7 years ago by cocchi.e89 ▴ 260

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It looks like singletons should be thrown out by FilterIntervals according to the documentation. Are you using an outdated version of GATK by any chance? There was an issue for a similar error on the github repo for GATK (resolved as of June 2020).

ADD REPLY • link 3.7 years ago by newbio17 ▴ 360

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yes that was the problem! Thank you so much @newbio17

ADD REPLY • link 3.7 years ago by cocchi.e89 ▴ 260

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