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A few options (feel free to add more):
- Continue to use GATK 3.6 CombineVariants in Somatic/Multi-Caller SNV workflows
- Use GATK4 MergeVCFs (or similar) and drop the `set` annotation from any fi…
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Hi Nalini,
I was playing around with this package. Thanks a lot providing these R bindings! Much appreciated.
Do you have by any chance an example for iterating through a GATK4 GenomicsDBImport …
lima1 updated
4 years ago
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### Is your feature request related to a problem? Please describe
- [x] bedtools/merge
- [x] bedtools/sort
- [x] cat/fastq
- [x] custom/dumpsoftwareversions
- [x] ensemblvep/vep
- [x] fastqc
- [x] ga…
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Small example.
```
$ cat ../tester.config
#SampleID LabSampleID SeqCentre Library(default=1)
LS24 OSCC_8-P AGRF
LS25 OSCC_9-P AGRF
LS6 OSCC_8-N A…
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### Which type of feature are you implementing?
- [X] I have selected (at least) one of the following `Label` for the feature
### Is there an existing issue / PR for this?
- [X] I have search…
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I'm trying to update gatk4's bioconda recipe to include gcnvkernel (a python package required for gatk4's germline cnv caller). However, when adding gcnvkernel to the requirements and introducing an i…
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### Description of the bug
Hi,
I am getting the following error. Can you please help ?
Thanks
-[nf-core/rnavar] Pipeline completed with errors-
Error executing process > 'NFCORE_RNAVAR:R…
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### Description of feature
i am attempting to install a subworkflow from a custom repository, but i am having issues installing the missing modules from the nf-core/modules repo:
```
$ nf-core subw…
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### Description of feature
I started a sarek run (`v3.4.2`) providing a custom reference in the form of a bgzipped FASTA. The run from FASTQs started normally and did not run into any errors until th…
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We are running joint-discovery-gatk4 in slurm with Cromwell 46.
Only a small fraction of the shards are being processed concurrently.
What adjustments can be made to process more or all shards …
ghost updated
4 years ago