Difference between revisions of "Raremetal Incoming updates"
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==Finished in test version== | ==Finished in test version== | ||
* '''Optimization for unbalanced studies (Jingjing Yang)''' | * '''Optimization for unbalanced studies (Jingjing Yang)''' | ||
| − | * | + | * Reduced running time when reading over 10,000s individual genotype from vcf |
| + | * Fixed seg fault in SNP HWE test when sample size > 40k | ||
* A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC. | * A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC. | ||
** This has been fixed on CSG cluster but not in 4.13.8 release. | ** This has been fixed on CSG cluster but not in 4.13.8 release. | ||
Revision as of 15:21, 8 July 2016
Main Wiki Page
Finished in test version
- Optimization for unbalanced studies (Jingjing Yang)
- Reduced running time when reading over 10,000s individual genotype from vcf
- Fixed seg fault in SNP HWE test when sample size > 40k
- A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC.
- This has been fixed on CSG cluster but not in 4.13.8 release.
Incoming update
- Add an option to store group file from vcf
- Take snpeff as annotation input
- When no conditional variant is available, warning is generated but not written to log file.
- SKAT conditional analysis misses the last 3 column names. They should be cond_statistics, cond_pvalue_davis, cond_p_value_liu.
- enable reading from .gz annotated vcf
- add SKAT-O
- solve the numeric issue of lambda = 0 in SKAT
- In conditional analysis, when cov matrix between the test variant and its conditioned variants is not invertible, MathSVD still tries to invert that matrix and that leads to weird conditional p values.
