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bigdatagenomics / avocado

A Variant Caller, Distributed. Apache 2 licensed.
http://bdgenomics.org/projects/avocado/
Apache License 2.0
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[AVOCADO-253] Add joint variant caller, direct save to VCF. #266

Closed fnothaft closed 6 years ago

fnothaft commented 6 years ago

Resolves #199, #253. Adds back a joint variant caller that computes rolled up variant level statistics and that saves directly out to VCF. This uses a binomial prior based on the alternate allele frequency to update the genotypes. We use the posteriors to generate the variant quality score.

AmplabJenkins commented 6 years ago

Test FAILed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/211/

Build result: FAILURE

GitHub pull request #266 of commit 71f0e3e20a56ebb549470159cb4a98047089f566 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) in workspace /home/jenkins/workspace/avocado-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/avocado.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/266/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 1e39b43d08478a1cd9446a41270d58820e652a38 # timeout=10Checking out Revision 1e39b43d08478a1cd9446a41270d58820e652a38 (origin/pr/266/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 1e39b43d08478a1cd9446a41270d58820e652a38First time build. Skipping changelog.Triggering avocado-prb » 2.3.0,2.11,2.0.0,centosTriggering avocado-prb » 2.3.0,2.10,2.0.0,centosTriggering avocado-prb » 2.6.0,2.11,2.0.0,centosTriggering avocado-prb » 2.6.0,2.10,2.0.0,centosavocado-prb » 2.3.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.3.0,2.10,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.11,2.0.0,centos completed with result FAILUREavocado-prb » 2.6.0,2.10,2.0.0,centos completed with result FAILURE Test FAILed.

AmplabJenkins commented 6 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/212/ Test PASSed.