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**Background**
There are 4 types of controls in the Varchamp data: transfection control, positive control (morphology), positive control (localization), and negative control (morphology). We are revi…
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**Is your feature request related to a problem? Please describe.**
The splice region is based on the sequence ontology setting. However, ACMG 2021 recommends different settings.
**Describe the…
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Using the files from Brandi, there are significant differences between the variants when loaded vs when called in BRAF. In particular, the loaded variants include a high impact, clinVar pathogenic sto…
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Consider the following pattern:
(subject:gene)(object:disease)
Where relation is one of:
1. pathogenic
2. likely pathogenic
3. has phenotype
4. marker/mechanism
5. contributes to
...
In…
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Currently we infer human gene to phenotype annotations by making the join
gene - disease (through a variant)
disease - phenotype
With some minor filtering of gene disease associations for marker…
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I'm trying to figure out why PM1 is scored as 1 for a variant. The variant is:
(hg19) 11:36615436C>T - RAG2 NM_001243786:exon3:c.G283A:p.G95R
I checked the PM1 check function:
```
def check_PM1(…
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If I'm in a gene and select a variant that is not in the list of prioritized variants at the left, I can still mark this as Significant, but:
1. The badge under findings only counts the variants in t…
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Right now it returns variants that are over certain specified frequency thresholds in gnomad. But for pathogenic thresholds we want to do the reverse, returning those less than the threshold. So we ne…
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Right now, the TRUE or FALSE variant screening results for trio analysis include parent-child inheritance checks, as well as other criteria that make a variant suspicious. However, for followup analys…
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Dear Professor Damiansm, recently I recognized the Exomiser, and I want to try analyzing my WGS data, I'm not a bio information student, so it's kind of hard for me to install the program, but I did!…
lpsyy updated
8 months ago