Raremetal Incoming updates: Difference between revisions
From Genome Analysis Wiki
Jump to navigationJump to search
| Line 6: | Line 6: | ||
* '''Optimization for unbalanced studies (Jingjing Yang)''' | * '''Optimization for unbalanced studies (Jingjing Yang)''' | ||
* Reduce running time when reading over 10,000s individual genotype from vcf | * Reduce running time when reading over 10,000s individual genotype from vcf | ||
* 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== | ==Incoming update== | ||
Revision as of 12:56, 8 July 2016
Main Wiki Page
Finished in test version
- Optimization for unbalanced studies (Jingjing Yang)
- Reduce running time when reading over 10,000s individual genotype from vcf
- 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
- 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
