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Dear Sigve
I wondered how PCGR deals with the more generic entries in CIViC, e.g. https://civicdb.org/events/genes/1/summary/variants/512/summary#variant does not have a specific chromosomal entry,…
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Having just annotated a candidatesSV.vcf from MANTA with VEP using the command below, I started Scout with a single case given the path to the annotated vcf and ran into the issue seen in Scouts outpu…
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Our initial ingest of ClinVar (see #7) used a tsv file that was missing much of the data only captured in their XML dumps. Our second pass will leverage the XML data, and include full evidence and pr…
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Hi,
Thanks for providing this tool and source code. The output looks great!
Is the license for this software open? If so, any guidance on the modifying the software to generate a summary of gener…
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Hi Sigve,
Thanks a lot for pushing the new release with all the fixes!
I'm running into another one unfortunately. `pcgr.R` fails with the following error:
```
pcgr.R E145__PRJ180035_E145-T0…
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The AC Maintenance Group will hold a Google Hangout call on Wednesday, May 2 from 18:00 to 19:00 UTC. The meeting will focus primarily on two issues: looking at the issues in the tracker to decide wh…
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The ACMG guidelines argue against use of the terms "mutation" and polymorphism. To be more consistent with these guidelines we could rename our `Variant Origin` values as follows:
Somatic mutation…
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**Prerequistes:**
- Your organization must be registered in Submission Portal before you can submit your variant data
- Variant-level not case-level
- Single variants or a set of variants (such as …
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We would also want to change the field to be a typeahead.
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Two things that are somewhat urgent:
1. I am trying to edit the list of ACMG evidence codes for an assertion:
https://civic.genome.wustl.edu/events/assertions/4/edit/basic
I am getting an error …