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This was posted by an external user:
I am harmonizing WGS data for the GREGoR consortium using the WGS single sample workflow (in dragen_mode) on AnVIL. I've hit a parsing error when reprocessing …
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…
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I noticed that AA can work with tumor-only WGS data since it was tested on the cell line data. I am just wondering what would be the benefits if giving with paired normal WGS as well.
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**User story**
As PSD, we would like to create configuration and integration test for the EMSeq branch of the LCM Triomics WGS/EMSeq pipeline to enable parallel development of the EMSeq branch of the…
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Dear Tcell ExTRECT team,
I have some whole-genome sequencing (WGS) data sequenced at a decent coverage (50x). Can I apply this tool to WGS data and get the t cell infiltration fractions?
Thank…
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Dear all,
I'm here for the first time in the community and have been trying for some time to obtain a pangenome to use as a reference for mapping short reads using `vg giraffe` and subsequent varia…
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Can snvstory take WGS data? Would it be enable by adjusting the defualt --mode WES to WGS?
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Thanks for your great work.
I have been testing this tool the last couple of days and wondering if there are optimal sites to select /subset for the input vcf ?
A large vcf would require lots of mem…
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### Description of the bug
Hi,
I ran the pipeline (`3.1.2`) for a bunch of tumor-only WGS samples. CNVkit reference bed files have both target and antitarget with improper bin counts:
```
wc -l *.…
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Hello,
I would like to thank you for such an incredible and well-documented resource, which is way better than the DNAnexus'es own pipelines/instructions. I was wondering if you have figured how to …