jamesemery

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

#carrot(GATK HaplotypeCaller vs Nightly Test, VariantCallingCarrot.gatk_docker, )

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrot.gatk_docker, )

@droazen I fixed the tests. Can you take a look? I know you have opinions

@ilyasoifer Looks like this user got tricked by some of the flow based annotations that don't work on their data. I would like to cut down on the risk that...

A command line that triggered the crash in our testing: ``` gatk HaplotypeCaller -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta -I gs://broad-dsde-methods-dragen/reprocessed_data_v3.7.5_masked/CH1_CHM13_WGS1/CH1_CHM13_WGS1.bam -L /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/109scattered.interval_list -O CH1_CHM13_WGS1.vcf.gz --pileup-detection --pileup-detection-absolute-alt-depth 0 --pileup-detection-bad-read-tolerance 0.4 --pileup-detection-enable-indel-pileup-calling --pileup-detection-active-region-phred-threshold 3.0 --use-pdhmm...

Hey @brianjohnhaas. I'm not quite sure i fully understand what we can change to help you here. However there is a feature you might not be aware of in the...

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )