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### Description of the bug
Hi,
This is about the GATK resource bundle but I am opening a bug report here because I encounter this while using this pipeline.
dbSNP138 has the wrong reference alle…
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**Describe the issue**
When running PureCN with my segmentation and VCF files, I encounter an error that says "Segmentation and VCF do not overlap." This stops the execution of the program.
**To R…
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As part of the Variant Page effort, we have discussed to start developing the first two widgets (sample data has been shared on slack):
- [x] ClinVar
```
{
"alleleOrigins": [
"germli…
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Hi,
Here I report a germline SNV which called as an somatic SNV.
```
chr7 150556055 . CG GC 266 PASS STATUS=Germline;SAMPLE=DN2003754SLZAA02;TYPE=Complex;DP=…
Gerde updated
3 years ago
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Hi there,
I have been using bamsurgeon to simulate germline copy number changes. I am inserting deletions and duplications from size ranges of 100bp to 10Mb.
One of my target sizes is 5Kb and w…
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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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`chr19 53167781 Minda_72 N . PASS SVLEN=1392;SVTYPE=DEL;SUPP_VEC=ILL_MantaDEL:2:77966:88630:0:0:0,PB_ID_62452_2,ONT_ID_51239_2,PB_severus_DEL3365,ONT_severus_DEL3818,ILL_1452158581:2
`
https://v2.ge…
jzook updated
1 month ago
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Dear all, I am using CNVkit to analyse exome sequencing data (germline samples) in order to find new copy number variants. For the pipeline analysis I followed all the found suggestions for germline s…
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I am running Canvas in a docker container using the hg19 reference files from the S3 link.
I am trying to call Canvas using variants called by strelka/starling on a shallow WGS (7 fold) dataset:
…
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Note krub, please help filx the order of filter using the guideline below
1. Keep all known pathogenic variants from ClinVar
2. Filter on impact on gene function, using VEP IMPACT Prediction, keep…