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As a TL I would to check the report consistency, identify and flag inconsistencies so that we can improve confidence in the report.
**Acceptance Criteria**
- [ ] Identify report rows where the m…
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We've been asked whether the search box support the drug classification(PARP1 inhibitors for instance). To support this feature, we need to have a reliable data source to keep the list up to date. Hem…
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https://www.biorxiv.org/content/early/2018/03/03/275628
> The diagnosis of multidrug resistant and extensively drug resistant tuberculosis is a global health priority. Whole genome sequencing of cl…
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Hi. I'm trying to run CopywriteR with some BAM files from targeted sequencing. We target 75 genes, get around 3-6M reads, and have around 40-70% off-target. When I try to run the software, I get the f…
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## Bug Report
### Affected tool(s) or class(es): Mutect2
### Affected version(s)
gatk 4.2.5
### Description
Like most use cases, I acquired a high-confidence, "consensus" VCF from a large …
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I got the following errors when running CNV_radar.R
I followed the previous steps exactly as stated in the manual.
Please advise how I should fix the bug.
Thanks.
[2021-01-22 22:46:12] - r…
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Hallo,
I have a WGS sample generated from an oral mucosa swap, sequenced with high coverage (150x) and mapped against GRCh38. Running telomerecat I get very low read values and a very low telomere …
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Add a warning that -*-protocol options and seq_type differ (at least for tumour). To ensure seqtype WXS doesn't get WGS as SAMPLE protocol set in the VCF.
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue for this…
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Thanks a lot
I am trying to run `mutect2` in **tumour-only** mode for which I need a panel of normal (PON)
I have tried **somatic-hg38_1000g_pon.hg38.vcf.vcf** which gives
`./gatk Mutect2 -R…