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Hi,
Thank you so much for your effort in developing and maintaining such a wonderful tool!
I am currently working on using WGS sequencing data for CNV calling, but I don’t have any normal samp…
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Hello I am new using Centrifuge. I am downloading now the databases and indices for complete genomes and nt/nr NCBI database. I was just wondering if it would be possible to include also a WGS databas…
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### Description
In conjunction with developing a PR for changing filters and settings for variants called with Manta, I reached out to one of our customers to ask if they were aware of any WGS cases …
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Hello,
Could you point me to a proper VCF to do snp-pileup on WGS for mm10/GRCm38?
I downloaded [00-All.vcf.gz](https://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/00-All.vcf.gz) but …
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This attempted WGS/UTM conversion tends to throw a lot of errors:
https://github.com/LBNL-UCB-STI/beam/blob/8a428b9e72f6c68e2f4832f4a305ff32e0248437/src/main/scala/beam/utils/scenario/UrbanSimScena…
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### Description of the bug
As a minimal example, I am locally (on a system with 24 cores and 128 GB RAM) running joint germline with just two WES samples with this nextflow.config file
process {
…
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### Overview
This refreshes DIF repo templates for groups and work items, along with instructions.
### TSC To Review
- [x] Review OG repo template / instructions
- Repo: https://github.com/dece…
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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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I have a multi-sample vcf and I'd like to plot a subset of these as individual samples using MultiQC (similar to your WGS example report). I've run GATK VariantEval (with `-ST Sample -noEV -EV TiTvVar…
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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 *.…