gemini-variation

When it comes to reporting the impact it is reported according to the most severely impacted

Hi, Not sure if you solved this already, but I recently ran into the same problem. The culprit in my

Sure thing - you can use "WHERE gene IN ('BRCA1', 'TP53', 'ATM', '

Did this release come out officially? So if we download and install via: wget https://github.com/

Hello! There is a new release of gnomAD, version 2.1. Is there some way how it can be added to the

Thank you so much! 在 2018年10月30日星期二 UTC+8上午12:03:28，Aaron Quinlan写道： In its default mode, the "

Hi all, I am wondering why following query wouldn't work? I am following the documents correctly

Hi all, What do we mean by {--permutations} option in calpha? How valuable it is? And what should be

Hi all, I calculated --nonsynonymous gene burden, in which total number of variants are 41420. If I

Just to clarify you should remove the “limit 5” clause, as that will solely report the first 5 rows

Hi there, Currently the gene burden test (gbt) given below provides burden of either "High

Hi there, I am estimating the pairwise distance between samples with query "gemini stats--mds

Hi, thanks for reporting this. would you open an issue on github and/or provide a simple test-case so

Hi Mary, you can see an example VEP command in the gemini documentation. Perhaps you didn't tell

You will want to use the same reference genome (fasta format) that you used for sequence alignment.

By they way CG -> CA is just G -> C, so it looks like VEP is noting that and calling it a

Hi Brent, It doesn't seem to me that that is the problem. Here is the command, subsequent error,

Hello GEMINI gurus, I have a couple of questions that I think are at the core of variant annotation

Hi, this is not possible directly, but you can output gt_alt_depths in the result and filter on that.

Hello, I am profiling gemini tumor/normal workflow on a multi-core system to find out performance

Hi Phil, sorry for the delay. currently, a DN+compound het will not be found correctly with gemini. I

Hi Jenn, I'm not sure why this error is occuring, but, the default gemini loader is only

Thank you Brent! I will follow yourindications. Andrea Il giorno giovedì 1 marzo 2018 16:30:22 UTC+1,

Hi, Thanks for the quick response. Unfortunately this work around doesn't help... Would it be

You could open an issue on the vcf2db repo with a small example VCF and I'll have a look. This

We have put 2076 whole genomes into gemini. It can be slow for some queries, but it's workable.

That was really helpful... Thank you very much! On Friday, January 26, 2018 at 11:54:59 PM UTC+9,

Hi CJ, I also do the WGS trio analysis recently, I followed the GATK pipeline and use HaplotypeCaller

http://gnomad.broadinstitute.org/variant/X-20227510-TC On Friday, December 15, 2017 at 10:25:13 AM

I see that only gnomad exomes are included in gemini database. Any plans to include the complete