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### Description of feature
Hi!
I was trying out the `joint_germline` option, which produces a multi-sample VCF file from haplotypecaller. It would be helpful to have a similar feature for othe…
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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
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Hi
thanks for putting together these great learning resources.
Would it be possible to add the correct answers and some explanations to the exercises at the end of [intro lesson 00](https://gith…
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Hi,
I'm trying to use Pisces to call a tumour-only sample. I'm using the following command:
```shell
$ dotnet Pisces.dll -bam tumour.bam \
-CallMNVs false -g hs37d5 -gVCF false \
-i h…
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I'm attempting to run a HaplotypeCaller job that requires that the BAM and BAI file are in the same directory. However, for some reason Cromwell is putting the inputs into separate subdirectories. For…
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** New feature**
Add new flag `--germline-example` to `snappy-start-project`. Usage:
```
snappy-start-project --directory PATH_TO_PROJECT --germline-example
```
**Expected behaviour**
Scri…
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I have encountered the following error. I have tried both with out without --save_output_as_bam. It didn't help. I also ensured sufficient memory (256G) is available.
Thank you!
```
_-[nf-core/…
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Following on from https://github.com/umccr-illumina/dragen/issues/53
vc-enable-phasing is currently running by default in the somatic pipeline and generating FORMAT/PS tags
To enable combing SNVs …
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### Description of the bug
Dear All, I am facing a problem almost at the end of sarek version 3.1 for germline detection.
Could you please provide me assistance and help me to fix it?
Many Th…
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### Description of the bug
Hi,
I'm trying to run sarek with "mutect2" for variant calling.
Pipeline completes successfully, but the folder "output/variant_calling/" is empty.
It seems like proce…