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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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### Notice
There are many files need to be copied from biowulf to S3 in many different folders.
### Detail
Root Path in S3:
lix33/COVID19/UpstreamAnalysis/PostPrimaryRun/Data/10_11_2021/lo…
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Add email notification into the COVID Auto Framework.
It contains many useful info.
Please check the example below:
```
============ std_input_01_200_keytable ============
Good News …
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Hi @Z1ni,
Any chance you could add support for Halo Infinite Campaign?
# Game name: Halo: Infinite (Campaign)
## Game Pass info
### Game package name: Microsoft.254428597CFE2_8wekyb3d8bbwe
…
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### Description of feature
Hi, I was wondering if you guys have thought to give the pipeline an option to use variants called from a DNA-seq(typically wgs) pipeline to use as input into "ASE read cou…
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It would be useful if there was a version of the oisst monthly data (or a conversion function to create one) that matched the format of the bccm variables. Despite overlapping in time and space, it's …
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A common use case for the data returned by EDR query will be to generate a summary value from the data for the area and time of interest, adding **optional** support for basic data aggregation methods…
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Hi,
When I use read.maf to read maf file, but almost variants are silent(silent variants/all variants: **16874**/17013).
I am unsure about that is annotation problem or something.
`df = read.ma…
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### Description of feature
I have WGS data generated with a library prep that includes UMIs ([Claret Biosciences SRSLY for FFPE](https://www.claretbio.com/products/kits).
The current pipeline code d…
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**Describe the bug**
runVarpipeline.sh doesn't exist in the Docker image.
**Impact**
The README steps cannot be followed. A workaround is to download 'runVarpipeline.sh' from github and add durin…