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Opening an issue for a potential GLASS conda environment to further enhance reproducibility. Packages that need to be explicitly installed to get Snakemake workflows to work include:
snakemake `con…
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I want to use VG map alignment file to use with GATK4 haplotypecaller. In order to do that I used the instructions mentioned here (https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variati…
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Tool: GATK4 CollectAlignmentSummaryMetrics
Location:
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.3.0/picard_analysis_CollectAlignmentSummaryMetrics.php
- [x] CWL
- [x] T…
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Hi,
I've been running bcbio on a sample with matched tumor/normal (using the variant2 analysis pipeline), and I keep getting the following error on one specific region of the genome. Mutect2 runs f…
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Hello @sigven
Thank you for making `PCGR`.
I am just wondering that can I use `PCGR` for a `VCF` generated by `GATK4` germline workflow?
Best,
Tushar
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GATK4 depends on a beta release of Protocol Buffer 3.0.0, specifically "3.0.0-beta-1" because other versions break the tests depending on hadoop.dfs.minicluster.utils. Eventually, we must move up to a…
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Bcbio v1.2.0
### Steps to reproduce
[Install bcbio in Vagrant VM](https://github.com/bcbio/bcbio-nextgen/blob/master/scripts/vm/osx/vagrant_osx.sh) then
```shell
cd /vagrant/bcbio-nextgen
~/loc…
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I have a vcf obtained through gatk4 processing which I want to convert to a human-readable genotype format for downstream data processing. The vcf file has a mix of diploid, tetraploid and few hexaplo…
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**Describe the bug**
I am running octopus on ~40x coverage WGS NA12878 data. I am aligning to hs38(including all additional contigs). Octopus ran for ~20hrs before crashing with:
> terminate ca…
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We run SortSamSpark using gatk4.1.4.0.
We found that when running gatk, spark cluster only uses one worker, and other server wokers can't be used. What is the reason?
Thanks.
My command is:
ga…