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Hi Chris,
Thanks for making this fantastic package!
I am working on the colocalization analysis with fine mapping using eQTL and GWAS. And I got some questions when I use this package.
Curre…
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https://github.com/Snitkin-Lab-Umich/scripts/blob/bd327744ca96acad0a3084c504bd1ae80f76c565/variant_parser_functions.R#L67
How do we want to deal with variants that say WARNING_TRANSCRIPT_NO_START_C…
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Things to include in this release:
- [ ] Change how loqusDB params are provided in config file. The current situation is the following: Scout accepts the following loqus connection params:
- A dict…
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> Millions of human genomes and exomes have been sequenced, but their clinical applications remain limited due to the difficulty of distinguishing disease-causing mutations from benign genetic variati…
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via @jxchong cc @arq5x
A user may find a variant that is not itself associated with disease, but is in a gene known to be associated with the disease. There is no way to store or query this info in g…
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Currently, gene_wise simply counts variants in families, doesn't do any phasing. If we made it handle phasing as needed for comp_hets, then we could use the gene_wise machinery to drive all of the exi…
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## General
- Displaying numeric data:
- use numeric option in appropriate table columns (right-align, monospace font).
- format large integers with commas wherever appropriate
- round decimals w…
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I use these all the time when working directly against gemini.
http://gemini.readthedocs.org/en/latest/content/querying.html#gt-filter-filtering-on-genotypes
For example:
```
gemini query --header…
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Hello,
For gene-based analyses, I was wondering if it was possible to set a minimum allele count? For instance, I want to build bins using MAF < 1% and for the MAC to be at least 10 variants. Addit…
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Hi,
I am working on annotating large datasets, specifically Whole Genome Sequencing (WGS) VCF files, using the Variant Effect Predictor (VEP). However, the annotation process is taking significantl…