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gemini-variation
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gemini-variation
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Welcome to the GEMINI (
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mailing list.
This forum is for the GEMINI user community to discuss techniques, analysis approaches, problems, and bugs.
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1.
Gemini source code
2.
Gemini documentation
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H K
Mar 13
Comparing impacts within same severity group
When it comes to reporting the impact it is reported according to the most severely impacted
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Comparing impacts within same severity group
When it comes to reporting the impact it is reported according to the most severely impacted
Mar 13
P V Jithesh
,
Andrew O
2
5/24/19
Error annotating with HGMD PRO
Hi, Not sure if you solved this already, but I recently ran into the same problem. The culprit in my
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Error annotating with HGMD PRO
Hi, Not sure if you solved this already, but I recently ran into the same problem. The culprit in my
5/24/19
KS VN
,
Aaron Quinlan
2
4/29/19
Specifying multiple number of genes
Sure thing - you can use "WHERE gene IN ('BRCA1', 'TP53', 'ATM', '
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Specifying multiple number of genes
Sure thing - you can use "WHERE gene IN ('BRCA1', 'TP53', 'ATM', '
4/29/19
Brent Pedersen
,
phillip.a...@gmail.com
4
3/20/19
release prep
Did this release come out officially? So if we download and install via: wget https://github.com/
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release prep
Did this release come out officially? So if we download and install via: wget https://github.com/
3/20/19
pristanna
12/13/18
gnomAD release 2.1
Hello! There is a new release of gnomAD, version 2.1. Is there some way how it can be added to the
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gnomAD release 2.1
Hello! There is a new release of gnomAD, version 2.1. Is there some way how it can be added to the
12/13/18
yuanxia...@gmail.com
,
Aaron Quinlan
3
10/29/18
A problem on GEMINI de_novo function
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 "
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A problem on GEMINI de_novo function
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 "
10/29/18
ehsan ullah
10/15/18
query for a specific region-following documentation but returns zero variants.
Hi all, I am wondering why following query wouldn't work? I am following the documents correctly
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query for a specific region-following documentation but returns zero variants.
Hi all, I am wondering why following query wouldn't work? I am following the documents correctly
10/15/18
ehsan ullah
10/6/18
c-alpha test- permutations
Hi all, What do we mean by {--permutations} option in calpha? How valuable it is? And what should be
unread,
c-alpha test- permutations
Hi all, What do we mean by {--permutations} option in calpha? How valuable it is? And what should be
10/6/18
ehsan ullah
9/27/18
Gene burden test and number of variants.
Hi all, I calculated --nonsynonymous gene burden, in which total number of variants are 41420. If I
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Gene burden test and number of variants.
Hi all, I calculated --nonsynonymous gene burden, in which total number of variants are 41420. If I
9/27/18
burcd...@gmail.com
,
Aaron Quinlan
4
9/21/18
sample query for the variants in a particular gene?
Just to clarify you should remove the “limit 5” clause, as that will solely report the first 5 rows
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sample query for the variants in a particular gene?
Just to clarify you should remove the “limit 5” clause, as that will solely report the first 5 rows
9/21/18
ehsan ullah
9/14/18
Gene burden test options
Hi there, Currently the gene burden test (gbt) given below provides burden of either "High
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Gene burden test options
Hi there, Currently the gene burden test (gbt) given below provides burden of either "High
9/14/18
Athina
9/7/18
gemini stats --mds
Hi there, I am estimating the pairwise distance between samples with query "gemini stats--mds
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gemini stats --mds
Hi there, I am estimating the pairwise distance between samples with query "gemini stats--mds
9/7/18
gni...@gmail.com
,
Brent Pedersen
2
8/27/18
HGNC nomenclature
Hi, thanks for reporting this. would you open an issue on github and/or provide a simple test-case so
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HGNC nomenclature
Hi, thanks for reporting this. would you open an issue on github and/or provide a simple test-case so
8/27/18
Mary Makarious
,
Brent Pedersen
5
8/23/18
Issues working with VCF2db
Hi Mary, you can see an example VEP command in the gemini documentation. Perhaps you didn't tell
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Issues working with VCF2db
Hi Mary, you can see an example VEP command in the gemini documentation. Perhaps you didn't tell
8/23/18
ninn...@gmail.com
,
Aaron Quinlan
2
8/14/18
Which reference to use for normalization
You will want to use the same reference genome (fasta format) that you used for sequence alignment.
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Which reference to use for normalization
You will want to use the same reference genome (fasta format) that you used for sequence alignment.
8/14/18
Shantanu Kumar
,
Brent Pedersen
3
8/3/18
synonymous mutation reported as insertion by GEMINI
By they way CG -> CA is just G -> C, so it looks like VEP is noting that and calling it a
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synonymous mutation reported as insertion by GEMINI
By they way CG -> CA is just G -> C, so it looks like VEP is noting that and calling it a
8/3/18
Michele Mehaffey
,
Brent Pedersen
3
7/30/18
Not able to amend gemini db
Hi Brent, It doesn't seem to me that that is the problem. Here is the command, subsequent error,
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Not able to amend gemini db
Hi Brent, It doesn't seem to me that that is the problem. Here is the command, subsequent error,
7/30/18
phillip.a...@gmail.com
7/24/18
Allelic primitives and overlapping genes
Hello GEMINI gurus, I have a couple of questions that I think are at the core of variant annotation
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Allelic primitives and overlapping genes
Hello GEMINI gurus, I have a couple of questions that I think are at the core of variant annotation
7/24/18
phillip.a...@gmail.com
2
6/25/18
Filtering on ref/alt depths within built-in analysis tools
Hi, this is not possible directly, but you can output gt_alt_depths in the result and filter on that.
unread,
Filtering on ref/alt depths within built-in analysis tools
Hi, this is not possible directly, but you can output gt_alt_depths in the result and filter on that.
6/25/18
Ramachandra CN
6/22/18
tumor-normal workflow
Hello, I am profiling gemini tumor/normal workflow on a multi-core system to find out performance
unread,
tumor-normal workflow
Hello, I am profiling gemini tumor/normal workflow on a multi-core system to find out performance
6/22/18
phillip.a...@gmail.com
,
Brent Pedersen
2
5/21/18
de novos incorporated into compound het model
Hi Phil, sorry for the delay. currently, a DN+compound het will not be found correctly with gemini. I
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de novos incorporated into compound het model
Hi Phil, sorry for the delay. currently, a DN+compound het will not be found correctly with gemini. I
5/21/18
Jenn Chin
,
Brent Pedersen
2
4/3/18
ValueError: Processing failed on GEMINI chunk load
Hi Jenn, I'm not sure why this error is occuring, but, the default gemini loader is only
unread,
ValueError: Processing failed on GEMINI chunk load
Hi Jenn, I'm not sure why this error is occuring, but, the default gemini loader is only
4/3/18
Andrea Spinelli
,
Brent Pedersen
3
3/1/18
update annotations
Thank you Brent! I will follow yourindications. Andrea Il giorno giovedì 1 marzo 2018 16:30:22 UTC+1,
unread,
update annotations
Thank you Brent! I will follow yourindications. Andrea Il giorno giovedì 1 marzo 2018 16:30:22 UTC+1,
3/1/18
Anselm Hoppmann
,
Brent Pedersen
3
2/22/18
Custom annotations in "Format" column
Hi, Thanks for the quick response. Unfortunately this work around doesn't help... Would it be
unread,
Custom annotations in "Format" column
Hi, Thanks for the quick response. Unfortunately this work around doesn't help... Would it be
2/22/18
Parkes Kendrick
,
Brent Pedersen
2
2/1/18
vcf2db without samples
You could open an issue on the vcf2db repo with a small example VCF and I'll have a look. This
unread,
vcf2db without samples
You could open an issue on the vcf2db repo with a small example VCF and I'll have a look. This
2/1/18
Aurel Beliard
,
Brent Pedersen
2
2/1/18
size limit of gemini db
We have put 2076 whole genomes into gemini. It can be slow for some queries, but it's workable.
unread,
size limit of gemini db
We have put 2076 whole genomes into gemini. It can be slow for some queries, but it's workable.
2/1/18
alka...@gmail.com
,
Brent Pedersen
3
1/28/18
Building DBs for gemini?!!
That was really helpful... Thank you very much! On Friday, January 26, 2018 at 11:54:59 PM UTC+9,
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Building DBs for gemini?!!
That was really helpful... Thank you very much! On Friday, January 26, 2018 at 11:54:59 PM UTC+9,
1/28/18
CJ Yoon
, …
Devin Liu
4
1/24/18
gemini builtin functions not compatible with merged vcf
Hi CJ, I also do the WGS trio analysis recently, I followed the GATK pipeline and use HaplotypeCaller
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gemini builtin functions not compatible with merged vcf
Hi CJ, I also do the WGS trio analysis recently, I followed the GATK pipeline and use HaplotypeCaller
1/24/18
Sergey Naumenko
2
12/15/17
Please add gnomad_num_hemi
http://gnomad.broadinstitute.org/variant/X-20227510-TC On Friday, December 15, 2017 at 10:25:13 AM
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Please add gnomad_num_hemi
http://gnomad.broadinstitute.org/variant/X-20227510-TC On Friday, December 15, 2017 at 10:25:13 AM
12/15/17
Javier Simón-Sánchez
,
Brent Pedersen
4
12/15/17
aaf_exac_all annotation seems to be wrong
I see that only gnomad exomes are included in gemini database. Any plans to include the complete
unread,
aaf_exac_all annotation seems to be wrong
I see that only gnomad exomes are included in gemini database. Any plans to include the complete
12/15/17