-
I recently started testing using a LOCAL to capture and remove platform-specific false positive variants. Basically, we have exomes for about 1000 individuals and sometimes we find "novel" variants (…
-
Dear gemini team,
I use gemini very frequently and it is an awesome tool for variant prioritization within large databases. However, one thing I could not find out yet is how to use the gt.alt.freq…
-
Dear Joelle
We're using Regenie to perform standard gene-level analyses (burden, skato etc) from population-scale WES data.
We'd like to begin exploring testing entire pathways using the same me…
-
Based on a survey of the variant types used in CIViC as a starting point:
- SNVs (single nucleotide variants). e.g. `R175H`
- MNVs (e.g. dinucleotide variants). e.g. `VHL c.364_365GC>AT`
- Insert…
-
We need to pull a series of data to inform which genes to look for variants in.
There is a[ google doc here](https://docs.google.com/spreadsheets/d/1yX-5sfrC3vrahf4_k7-5rl4Oqzm853ollIMmUo1PTc0/edit…
-
We ran into this with searching ASCO abstracts vs PubMed records and will run into it again when implementing advanced search of suggested changes (ie: changes to Genes will have different available f…
-
To reproduce:
Find variants in the CRT gene in the HB3 x DD2 Cortex callset, click on the K76T mutation, click on "Browse Genotypes". See the following...
![image](https://f.cloud.github.com/assets/…
-
I used Saute to assemble a reference fasta sequence '>CRYPT1020_1' from Illumina reads. I got 2 assemblies:
>CRYPT1020_1:1:1:87926 2 4 1
>CRYPT1020_1:1:2:87918 2 3 1
Why are there 2 assemblies an…
-
**Is your feature request related to a problem? Please describe.**
Carrier screening of both parents for compound heterozygous variants is currently not possible (if the index does not carry both of …
-
# Describe the bug
We have observed that ```ivar variants``` can generate false positive variant calls for SARS-CoV-2 genomes that contain insertions or deletions. Here is an example from a private…