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MSID: 94485
Version: 2
Preprint DOI: https://doi.org/10.1101/2023.05.24.542099
## Step 1. Awaiting reviews
**Editorial to post reviews via hypothesis**
**Useful links:**
- DocMap: https://data-hu…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Description of the Bug/Issue
Hi all,
First, thanks for all the work being done on this pipeline.
I'm ha…
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### Title
Niviz: Configurable quality control image generation and rating
### Leaders
Jerrold Jeyachandra @jerdra
### Collaborators
None
### Brainhack Global 2021 Event
BrainHack …
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## **Describe the bug**
It seems the pipeline has an error on the qc step.
* Started troubleshooting workflow: id=65302236-00d0-4f5c-af80-47836f267413, status=Failed
* Found failures JSON object.
…
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When 2 or more alleles are detected at the same gene, whether those alleles are new or existing, this should appear in the results.
As per today it doesnt. Moreover in this case the CC group must re…
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so that sge does not bog down...probably cap it at 15k samples. in that event, need to send let user know that pipeline becomes a 2 stage process and the qc report generation needs to be done a separa…
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We're currently adding all alignments into the ARG regardless of how much missingness there is. We currently have a max_masked_sites_per_sample of 6535 (2021-02-26) which seems quite high.
What wou…
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## For UI issues
* Tool: Picard
* Version: 2.19.0
### Description
WGS pipelines are long and therefore can have a high degree of variability across runs. Picard has many commands for generatin…
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I have installed the package as detailed in the Tutorial of RNA-seq tumor immunity analysis using Google Cloud Platform on my institute’s HPC. The pipeline completes the star aligning, salmon and down…
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- [ ] have FFT tested and incorporated or rejected from pipeline, with according QC, and also tested with subsets of nuisance correction (ie, nuisance correction without CompCor, tested using FFT then…