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224 bytes added
, 12:52, 14 March 2019
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| + | [[Category:RAREMETAL]] |
| + | [[Category:RAREMETALWORKER]] |
| ==Main Wiki Page== | | ==Main Wiki Page== |
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| * [[RAREMETAL_Change_Log | RAREMETAL Change log]] | | * [[RAREMETAL_Change_Log | RAREMETAL Change log]] |
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− | ==Finished in test version== | + | ==Reporting a bug== |
− | * '''Optimization for unbalanced studies (Jingjing Yang)'''
| + | Please report issues at our GitHub repository [https://github.com/statgen/raremetal/issues issue tracker]. When possible, include your platform (Ubuntu, CentOS, Mac OS, etc), as well as any relevant commands and output that can help us to identify the problem. |
− | * Reduce running time when reading over 10,000s individual genotype from vcf
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| ==Incoming update== | | ==Incoming update== |
| + | * Add an option to store group file from vcf |
| * 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. |
− | * SKAT conditional analysis misses the last 3 column names. They should be cond_statistics, cond_pvalue_davis, cond_p_value_liu.
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− | * A seg fault: sometimes you only have very few variants but raremetal still tries to calculate GC.
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− | ** This has been fixed on CSG cluster but not in 4.13.8 release.
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| * enable reading from .gz annotated vcf | | * enable reading from .gz annotated vcf |
| * add SKAT-O | | * add SKAT-O |
| * solve the numeric issue of lambda = 0 in SKAT | | * 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''' |