Difference between revisions of "Raremetal Incoming updates"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 7: | Line 7: | ||
* Take snpeff as annotation input | * Take snpeff as annotation input | ||
* When no conditional variant is available, warning is generated but not written to log file. | * When no conditional variant is available, warning is generated but not written to log file. | ||
| − | |||
* enable reading from .gz annotated vcf | * enable reading from .gz annotated vcf | ||
* add SKAT-O | * add SKAT-O | ||
Revision as of 15:07, 27 November 2016
Main Wiki Page
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.
- 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.
- Optimization for binary traits
- Memory optimization for gene-based test in large panel
