GATK4_acnv problems

ChipChip 415M 4053Member, Broadie

Hi

We ran into some GATK4_acnv failures while processing StandUp2Cancer exomes this weekend using

gs://fc-099b74a5-b2e1-4f8c-8720-2ab7123fe631/ref_data/gatk-package-4.beta.1-local.jar

We've run this version of GATK4_acnv on hundreds of exomes without failing but this weekend three samples had failures. There were two types of failure messages. Two samples failed with stderr message:

java.lang.IllegalArgumentException: Must have a positive number of SNPs to perform SNP segmentation.

and one failure was a stderr message:

java.lang.IllegalArgumentException: additional variance must be positive.

Would a more recent gatk jar fix these issues? We are somewhat hesitant to
try new versions because we've done quite a bit of analysis already with this version and a switch of versions could trigger another round of work (i.e. ABSOLUTE reviewing). The common het sites were input as gs://firecloud-tcga-open-access/tutorial/reference/only_very_good_hets.tsv.

Is this sufficient information to diagnose the issue (@slee, @lichtens) or would Firecloud access to the SU2C workspace be needed to figure this out?

Thanks,

Chip and Arvind (@stewart, @aravi)

P.S. These hg19 bams were produced at Broad and seem to have reasonably decent coverage (~100x mean target coverage).

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