To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

GenotypeGVCF output

lsturmlsturm Member
edited September 2016 in Ask the GATK team

Hi,

I am running joint calling with GenotypeGVCF. The output from the program is being put into an "error" file. This file is being filled with gigabytes of lines similar to "WARN 18:38:59,655 ReferenceConfidenceVariantContextMerger - WARNING: remaining (non-reducible) annotations are assumed to be ints or doubles or booleans, but 0,0|0,0|0,0 doesn't parse and will not be annotated in the final VC." I used the GATK's Haplotype Caller to make my GVCFs. Is there any way to avoid all of this output, as it makes it hard to see if there were actually any errors during the call and is a large file that takes up a lot of space.

Thank you,
Luke

Tagged:

Issue · Github
by Sheila

Issue Number
1320
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

Sign In or Register to comment.