Minimac3 ChangeLog - Revision history

Santy.8128: /* Ver 2.0.1 (June 6, 2016) */

2016-06-07T02:24:24Z

Ver 2.0.1 (June 6, 2016)

← Older revision		Revision as of 22:24, 6 June 2016
Line 33:		Line 33:
	are over 1.0.		are over 1.0.
	4. Added <contig> in VCF header to make bcftools readable.		4. Added <contig> in VCF header to make bcftools readable.
			5. Added FILTER column for typed sites and only typed sites.

	==Ver 1.0.14 (April 15, 2016)==		==Ver 1.0.14 (April 15, 2016)==

2016-06-06T23:26:35Z

← Older revision		Revision as of 19:26, 6 June 2016
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	3. Changed definition of Estimated R-square so that no estimates		3. Changed definition of Estimated R-square so that no estimates
	are over 1.0.		are over 1.0.
			4. Added <contig> in VCF header to make bcftools readable.


	==Ver 1.0.14 (April 15, 2016)==		==Ver 1.0.14 (April 15, 2016)==

2016-06-06T23:01:36Z

Ver 2.0.1 (June 6, 2016)

← Older revision		Revision as of 19:01, 6 June 2016
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	3. Added a --lowMemory version that further reduces the memory usage		3. Added a --lowMemory version that further reduces the memory usage
	furhter by 33% (but takes 10% more time.		furhter by 33% (but takes 10% more time.

	Minor Changes:		Minor Changes:
	1. Fixed a minor bug in parameter estimation (--processReference)		1. Fixed a minor bug in parameter estimation (--processReference)

2016-06-06T23:00:44Z

@@ Line 13: / Line 13: @@
 Minimac3 Changes:
 --------------------------------------------------------------------------
 ==Ver 1.0.14 (April 15, 2016)==

2016-05-05T19:06:16Z

Ver 1.0.14 (April 15, 2016)

← Older revision		Revision as of 15:06, 5 May 2016
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	Fixed a bug in the makefile that was missing the g++ -O4		Fixed a bug in the makefile that was missing the g++ -O4
	optimization flag. As a result, the openmp version was		optimization flag. As a result, the openmp version was
	3-4 times slower than expected.		3-4 times slower than expected. Updated LibStatGen Library
			files to remove some warnings/errors.

	==Ver 1.0.13 (October 15, 2015)==		==Ver 1.0.13 (October 15, 2015)==

2016-04-15T04:23:02Z

Change Log Summary

@@ Line 13: / Line 13: @@
 Minimac3 Changes:
 --------------------------------------------------------------------------
 ==Ver 1.0.13 (October 15, 2015)==

2015-10-15T02:01:05Z

Ver 1.0.13 (October 15, 2015)

← Older revision		Revision as of 22:01, 14 October 2015
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	Updated the format of info file to report only REF and ALT		Updated the format of info file to report only REF and ALT
	alleles instead of Major and Minor allele. The usual .dose		alleles instead of Major and Minor allele. The ALT_Frq and
			MAF can be compared to find minor allele. The usual .dose
	and .hapDose file have been updated to report alternate al-		and .hapDose file have been updated to report alternate al-
	-llele dosage and NOT major allele dosage, like earlier ve-		-llele dosage and NOT major allele dosage, like earlier ve-

2015-10-15T02:00:05Z

Ver 1.0.12 (September 5, 2015)

← Older revision		Revision as of 22:00, 14 October 2015
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	--------------------------------------------------------------------------		--------------------------------------------------------------------------

	==Ver 1.0.12 (~~September 5~~, 2015)==		==Ver 1.0.13 (October 15, 2015)==

	Version : 1.0.12		Version : 1.0.13
	Author : Sayantan Das		Author : Sayantan Das
	Date : ~~September~~ 5, 2015		Date : October 5, 2015

	~~Added~~ --~~allTypedVariants option which adds variants which were~~		Updated the format of info file to report only REF and ALT
	~~typed ONLY to the imputed output files~~ and ~~imputes any missing~~		alleles instead of Major and Minor allele. The usual .dose
	~~values in such variants to the MAF~~. Also ~~fixed~~ a bug ~~with chr-~~		and .hapDose file have been updated to report alternate al-
	~~-omosome X~~ only ~~male samples. Also added~~ --~~rsid~~ option ~~to use~~		-llele dosage and NOT major allele dosage, like earlier ve-
	~~rs IDs of variants. Updated info file RefMAF~~ to ~~RefAF since it~~		-rsions of minimac. Also mended a bug related to variants
	~~gives~~ the ~~alternate AF and NOT minor AF~~.		that were typed only, while using --allTypedVariants option.
			Finally, added acknowledgements to David Hinds, for his
			immense help in making the code faster.

	==Ver 1.0.12 (September 5, 2015)==		==Ver 1.0.12 (September 5, 2015)==

2015-10-15T01:56:26Z

Change Log Summary

@@ Line 13: / Line 13: @@
 Minimac3 Changes:
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 ==Ver 1.0.12 (September 5, 2015)==

2015-09-18T16:54:28Z

Ver 1.0.12 (September 5, 2015)

← Older revision		Revision as of 12:54, 18 September 2015
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	values in such variants to the MAF. Also fixed a bug with chr-		values in such variants to the MAF. Also fixed a bug with chr-
	-omosome X only male samples. Also added --rsid option to use		-omosome X only male samples. Also added --rsid option to use
	rs IDs of variants.		rs IDs of variants. Updated info file RefMAF to RefAF since it
			gives the alternate AF and NOT minor AF.

	==Ver 1.0.11 (April 21, 2015)==		==Ver 1.0.11 (April 21, 2015)==