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Hello,
Thanks for this useful utility.
I have data in MAF format (NCBI build 37). I am trying to lift it over to hg38 using the following Crossmap (v0.6.6) command:
```
CrossMap maf b37ToHg38.…
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It will be important to standardize data for certain attributes by binding them to value sets. We identified a handful of places where we considered this (see below), and agreed on terms to be includ…
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Hi all.
As has been discussed previously we in Umeå has started to work on an extension that will enable 3rd party variant interpretation tools integration in scout. But we have also received fund…
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Clinical Significance - current clinical significance does not adequately support the needs for somatic variant information.
- Current set of values defined by LOINC
![image](https://github.com/Co…
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**Is your feature request related to a problem? Please describe.**
In a validation of the GMS Lymphoid panel there's been a few variants in the reference samples that were filtered out in the VCF d…
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Several mongo queries are really slow which occasionally can cause timeout issues for users.
The general issue are that many queries uses $and/$or statements which require mongo to evaluate all cas…
mhkc updated
10 months ago
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Should we consider an allelic requirement qualifier on variant pathogenicity interpretations that would allow us to capture how many copies of a variant would be required to cause the indicated diseas…
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### Background
Following Variation Set discussions at the Boston Plenary, it was decided that VR will only provide a model for **static** Variation Sets - as simple objects holding just an enumerated…
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Assertion descriptions will need to include references to internal CIViC entities and other resources e.g. EIDs, ACMG codes, PubMed articles, etc. Descriptions are intended to be a condensed rationale…
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Hi Sigven,
Thanks for this wonderful project.
Recently I use PCGR to get both HTML report and MAF.
It seems that the file input to vcf2maf isn't annotated, so most column are empty in the final…