Raremetal Incoming updates - Revision history

Abought: Link to issue tracker

2019-03-14T16:52:42Z

Link to issue tracker

← Older revision		Revision as of 12:52, 14 March 2019
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	* [[RAREMETAL_Change_Log \| RAREMETAL Change log]]		* [[RAREMETAL_Change_Log \| RAREMETAL Change log]]

			==Reporting a bug==
			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.

	==Incoming update==		==Incoming update==

2018-03-16T21:55:14Z

2016-11-27T19:07:39Z

Incoming update

← Older revision		Revision as of 15:07, 27 November 2016
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	* 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.
	* enable reading from .gz annotated vcf		* enable reading from .gz annotated vcf
	* add SKAT-O		* add SKAT-O

2016-11-27T19:07:19Z

Finished in test version

← Older revision		Revision as of 15:07, 27 November 2016
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	* [[RAREMETAL_Change_Log \| RAREMETAL Change log]]		* [[RAREMETAL_Change_Log \| RAREMETAL Change log]]

	~~==Finished in test version==~~
	* '''Optimization for unbalanced studies (Jingjing Yang)'''

	==Incoming update==		==Incoming update==

2016-07-19T12:41:22Z

Incoming update

← Older revision		Revision as of 08:41, 19 July 2016
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	* 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.		* 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'''		* '''Optimization for binary traits'''
			* '''Memory optimization for gene-based test in large panel'''

2016-07-17T16:07:39Z

Incoming update

← Older revision		Revision as of 12:07, 17 July 2016
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	* 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.		* 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 unbalanced studies'''
	* '''Optimization for binary traits'''		* '''Optimization for binary traits'''

2016-07-17T16:07:23Z

Incoming update

← Older revision		Revision as of 12:07, 17 July 2016
Line 15:		Line 15:
	* 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.		* 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 unbalanced studies'''
			* '''Optimization for binary traits'''

2016-07-14T17:10:58Z

Finished in test version

← Older revision		Revision as of 13:10, 14 July 2016
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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.
	** This has been fixed on CSG cluster but not in 4.13.8 release.

	==Incoming update==		==Incoming update==

2016-07-08T19:22:20Z

Finished in test version

← Older revision		Revision as of 15:22, 8 July 2016
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	* '''Optimization for unbalanced studies (Jingjing Yang)'''		* '''Optimization for unbalanced studies (Jingjing Yang)'''
	* Reduced running time when reading over 10,000s individual genotype from vcf		* Reduced running time when reading over 10,000s individual genotype from vcf
	* Fixed seg fault in SNP HWE test when sample size > 40k		* '''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.

2016-07-08T19:21:47Z

Finished in test version

← Older revision		Revision as of 15:21, 8 July 2016
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	==Finished in test version==		==Finished in test version==
	* '''Optimization for unbalanced studies (Jingjing Yang)'''		* '''Optimization for unbalanced studies (Jingjing Yang)'''
	* ~~Reduce~~ running time when reading over 10,000s individual genotype from vcf		* 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.