Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We ran into some GATK4_acnv failures while processing StandUp2Cancer exomes this weekend using
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.
P.S. These hg19 bams were produced at Broad and seem to have reasonably decent coverage (~100x mean target coverage).