-
CNVs, microsatellites and a variety of somatic variant representations have given rise to the notion of defining a variant grouping that is a set of variant instances (not necessarily equivalent) whic…
-
@chapmanb
1) I would like to run a trio analysis in whole exome samples. Can I use all callers (strelka2, deepvariant. vardict, gatk etc) for a trio analysis with samples having the same batch nam…
-
Hi all. On the May 6 VR call (and in Hinxton the week before), concerns were raised about scenarios in which a single discrete variant instance (e.g. `NP_478102.2:p.Ser73Arg`) might appear in more t…
-
http://bejerano.stanford.edu/mcap/
https://www.nature.com/articles/ng.3703
Method | Authors' Recommended Pathogenicity threshold | Misclassified known pathogenic variants
-- | -- | --
SIFT | <…
-
Hi -- I was able to successfully run CharGer, but all variants are classified as "Uncertain Significance." Is there a setting that must be tweaked for variant annotation to work correctly? I'm guessin…
-
There are often cases where a known pathogenic variant my occur more frequently in a population than the frequency cutoff filter is set to.
Enable the ability to specify variants which should pass …
-
If a variant has multiple clinsig values, for instance "Pathogenic/Likely pathogenic", it cannot be found using the CLINSIG-filter.
Multiple clinsig.values are stored in the database as a comma-sep…
-
try this heuristic
```
if (number of observed path vars > 2) {
LR =Pois(#observed vars | lambda=2) / Pois(#observed vars | lambda=#observed vars)
} else {
-- use existing score
}
```
This ne…
-
>It is also important, in the introduction, and indeed for the presentation of information in the collated database, for the authors to be clear that the variant interpretation processes for germline …
-
These terms has the same name and OMIM ID. Consider merge.
id: DOID:0080466
name: multiple congenital anomalies-hypotonia-seizures syndrome 2
id: DOID:0080139
name: multiple congenital anomali…