toil-vg
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vgteam
Distributed and cloud computing framework for vg
Hi guys, I follow the tutorial command in the wiki page [here](https://github.com/vgteam/toil-vg/wiki/Genotyping-Structural-Variants) for structral variants. when comes to the `toil-vg call`, the current toil-vg (v1.6.0) did not have these two...
https://github.com/vgteam/toil-vg/blob/99101f2b79a540c09c9774881807059b289b5d42/src/toil_vg/vg_vcfeval.py#L551 I've install the new sveval package from R. ```R BiocManager::install('jmonlong/sveval') ``` Change `min.cov` to `min.ol` could let the toil vdfeval work without issues I don't know how this will...
require(len(options.vcf_phasing) > 0, 'generating a GBWT requires a VCF with phasing information'). After delete `_phasing` it works again.
I am running into the following error with 1.6.2a1.dev415 and Python 3.6: ``` node003 2020-08-27 13:00:59,701 MainThread WARNING toil.leader: kind-run_merge_gams/instanceg9052nwo Traceback (most recent call last): node003 2020-08-27 13:00:59,701 MainThread WARNING...
The mkdir commands in the dragen jobs in vg_pedigree.py need directory existence checks.
The pedigree analysis workflow is hooked into the `analysis` subcommand which is too ambiguous in meaning. It should be more like `pedigree_analysis` or `pedigreeanalysis`, but the two-word subcommand name is...
The last couple merges to master have had CI time out [like this](https://ucsc-ci.com/vgteam/toil-vg/-/jobs/53277), although the corresponding PRs passed: ``` src/toil_vg/test/test_vg.py::VGCGLTest::test_17_sim_small_standalone_singularity ERROR: Job failed: execution took longer than 3h0m0s seconds ```