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We need a universal set of variant filters for downstream analyses, such as SKAT / Simreg / Phenogenon. Shall we create a new config file for filters, or just push them into `local.cfg` ?
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Hi!
I usually run rvtests for rare variant testing with no problems at all. However, only for some genes, I've been getting the following error message:
```
[INFO] Analysis begins with [ 15301 ]…
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Something akin to *skat* classification like:
- https://www.enasco.com/prod/images/products/D9/AC134838l.jpg
But instead of various animals that make the poo, have a classification system that i…
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Hi, I am getting the full range of covariate results in the output from the SKAT and Burden test. Is there any option to hide the covariate effect from the output. I tried hide-covar, but it does not …
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When I run my gene-based SKAT analyses, I get the following output file:
#GROUPNAME | NUM_VAR | VARs | AVG_AF | MIN_AF | MAX_AF | **STATISTICS** | PVALUE_DAVIES | PVALUE_LIU
AKR1C3 | 715 | | 0.0…
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Hi,
I am using the GENESIS package to perform a SKAT-O analysis on every chromosome, variants being aggregated by genes.
I am using the same code for all of the chromosomes, and it worked perfectl…
pjuge updated
9 months ago
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Investigation is needed to understand how a ManagedProperties object can be created and injected via a blueprint.
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Most of gene-level outputs are reasonable, but there are a few lines show "-nan" in Pvalue.
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Gene RANGE N_IN--geneFile ${geneF} --kernel skato
FORMATIVE NumVar NumPolyVar Q …
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Idee
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Simples Interface, welches ein Kartenspiel abbilden soll.
Das gewünschte Kartenspiel kann vorher ausgewählt werden (Poker, Skat, etc.).
Man kann dann Karten ziehen, bis der Kartenstapel le…
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Hi @joellembatchou,
So I'm running regenie for UKB data while using the burden/skat-o options.
I was wondering if there's any workaround to include variants in which the REF allele is actually …