GotCloud: Versions - Revision history

Mktrost: /* Version 1.16 (Full Release on 2/25/2015) */

2015-05-14T16:17:37Z

Version 1.16 (Full Release on 2/25/2015)

← Older revision		Revision as of 12:17, 14 May 2015
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	For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]		For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]

			== Version 1.17 (Full Release on 5/14/2015) ==
			Source can be downloaded from: https://github.com/statgen/gotcloud/releases/tag/gotcloud.1.17

			'''General'''
			* Add ability to run custom pipelines
			* Fix bug in libVcfVcfFile.cpp
			* Fix some compatibility issues for CentOS5

			'''Aligner'''
			* Add pipelines to run just recab & QC, and just QC.
			* VerifyBamID
			** Exclude ChrX & Y

			'''SnpCall'''

			'''Genotype Refinement'''

			'''Indel'''

			'''GenomeSTRiP'''


	== Version 1.16 (Full Release on 2/25/2015) ==		== Version 1.16 (Full Release on 2/25/2015) ==

Mktrost at 18:58, 26 February 2015

2015-02-26T18:58:10Z

← Older revision		Revision as of 14:58, 26 February 2015
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			__TOC__

	For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software\|Install GotCloud Software]]		For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software\|Install GotCloud Software]]
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	== Version 1.16 (Full Release on 2/25/2015) ==		== Version 1.16 (Full Release on 2/25/2015) ==
			Source can be downloaded from: https://github.com/statgen/gotcloud/releases/tag/gotcloud.1.16

	'''General'''		'''General'''

Mktrost: /* Version 1.16 (Full Release on 2/25/2015) */

2015-02-26T18:48:58Z

Version 1.16 (Full Release on 2/25/2015)

← Older revision		Revision as of 14:48, 26 February 2015
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	'''General'''		'''General'''
			* Update the default REF to hs37d5.fa (build 37 with decoy) and the default DBSNP_VCF to dbsnp version 142.
			** You can download an updated reference at: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142\|hs37d5-db142]] (ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz)
			* Upgrade perl scripts to use <code>/usr/bin/env perl</code> instead of <code>/usr/bin/perl</code> to make it compatible with more users
			* Upgrade to latest versions of libStatGen and bamUtil (versions 1.0.13)
			** Fixes bug in calculating the MD5s for the fasta in polishBam

			'''Aligner'''
			* Update default aligner to <code>bwa mem</code>
			** you can still use <code>bwa aln</code> (the previous default) by adding the following setting to your configuration file:
			**:<code>MAP_TYPE = BWA</code>
			* Upgrade to <code>bwa</code> version 0.7.12
			* No longer call <code>verifyBamID</code> with the <code>--verbose</code> option


			'''SnpCall'''

			'''Genotype Refinement'''

			'''Indel'''
			* Cleanup pipeline.pl to reduce errors in some versions of perl

			'''GenomeSTRiP'''

	== Version 1.15 (Full Release on 12/16/2014) ==		== Version 1.15 (Full Release on 12/16/2014) ==

Mktrost at 22:39, 25 February 2015

2015-02-25T22:39:35Z

← Older revision		Revision as of 18:39, 25 February 2015
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	For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]		For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]

			== Version 1.16 (Full Release on 2/25/2015) ==

			'''General'''



	== Version 1.15 (Full Release on 12/16/2014) ==		== Version 1.15 (Full Release on 12/16/2014) ==

Mktrost at 00:40, 17 December 2014

2014-12-17T00:40:38Z

← Older revision		Revision as of 20:40, 16 December 2014
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	For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]		For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]

			== Version 1.15 (Full Release on 12/16/2014) ==

			'''General'''
			* Rename BAM_INDEX to BAM_LIST
			* Change default REF_DIR
			* Add ref_dir and list as command-line options to all pipelines
			* Add bed-diff script to compare VCFs

			'''Aligner'''
			* By default, create BAM_LIST
			* Use SAMPLE instead of MERGE_NAME if MERGE_NAME is not specified in FASTQ_LIST
			* No longer require fastqs to end in 'fastq.gz' or 'fastq'
			* Rename INDEX_FILE to FASTQ_LIST and infer all fields except FASTQ1, FASTQ2, and either SAMPLE or MERGE_NAME
			* Change --numcs to --numjobs and what was --numjobs to --threads
			* Update to latest BWA
			** Update aligner to pass \t instead of tabs for the RG fieldto new version of BWA
			* By default, no longer store OQ

			'''SnpCall'''
			* Add validation that:
			** Each BAM has only 1 sample
			** BAM's sampleID matches id in BAM_LIST
			*** Use --ignoreSMcheck to disable this validation
			* Updated Exome/Targeted settings
			** Set TARGET_DIR and OFFSET_OFF_TARGET (0) in defaults
			** Remove WRITE_TARGET_LOCI and base it on whether or not UNIFORM_TARGET_BED/MULTIPLE_TARGET_MAP are set and either the loci file doesn't exist, is older than the bed, or was created by a different bed
			* Add validation that tabix in perl scripts succeed
			* Fix some bugs in glfFlex & add region option
			* Cleanup logs so they no longer spew to the screen
			* Add ext-filt option for single sample filtering
			* Add .OK file after vcflist file successfully created

			'''Genotype Refinement'''
			* Add validation that tabix in perl scripts succeed
			* Add .OK file after vcflist file successfully created

			'''Indel'''
			* Update default region settings
			* Move output directories to an "indel" folder

			'''GenomeSTRiP'''
			* Add a GenomeSTRiP pipeline

Mktrost at 13:18, 29 August 2014

2014-08-29T13:18:41Z

← Older revision		Revision as of 09:18, 29 August 2014
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	For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]		For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]


			== Version 1.14 (Full Release on 8/29/2014) ==

			'''General'''
			* Add initial beagle4 support (as a new pipeline)
			* Improve input validation
			** Add chromosome name consistency checks to all tools
			* Upgrade version of bgzf
			* Upgrade libStatGen to fix mergeBam issue.

			'''Aligner'''
			* Cleanup reading of fastq index/info file
			** ignore empty lines (generates a warning)
			** compress extra tabs/trim white space
			* Validate that BWA_QUAL and BWA_THREADS settings are properly formatted

			'''SnpCall'''
			* Replace glfMultiples with glfFlex
			* Validate format of BAM_INDEX file
			* Add INDEL_VCF as an alternate for INDEL_PREFIX for input indel vcfs that aren't split by chromosome.

			'''Genotype Refinement'''
			* Only run beagle/thunder with more than 1 sample

			'''Indel'''
			* mergeBams for a single sample as its own step (didn't work before)
			* Fix bug that it would fail if the list of files was too long
			* Add input validation
			* Validate format of BAM_INDEX file


	== Version 1.13 (Full Release on 7/15/2014) ==		== Version 1.13 (Full Release on 7/15/2014) ==

Mktrost: /* Version 1.13 (Full Release on 7/15/2014) */

2014-07-15T13:29:32Z

Version 1.13 (Full Release on 7/15/2014)

← Older revision		Revision as of 09:29, 15 July 2014
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	* Added a ldrefine test.		* Added a ldrefine test.

	'' Indel Calling'''		'''Indel Calling'''
	* Initial version of Indel Caller		* Initial version of Indel Caller
	** Still in testing phases, if you use, please provide feedback.		** Still in testing phases, if you use, please provide feedback.

Mktrost at 13:29, 15 July 2014

2014-07-15T13:29:13Z

← Older revision		Revision as of 09:29, 15 July 2014
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	For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]		For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems\|FAQ: Version Problems]]

			== Version 1.13 (Full Release on 7/15/2014) ==
			''' General '''
			* Cleanup runcluster
			* Upgrade to bamUtil v1.0.12a
			* Upgrade to libStatGen v1.0.12
			* Update README to add build instructions & wiki references

			'''Aligner'''
			* Increment to latest VerifyBamID

			'''Variant Calling'''
			* Update glfMultiples to handle when first glf is empty
			* Add check for the output file before creating the .OK file
			* VcfPileup - improve return codes
			* Write jobfiles into a sub-directory
			* Added a snpcall monitoring utility
			* VcfSplit - update to only append .gz in the vcflist if there was at least one file
			* Write start/stop timestamps into a logfile (generated by runcluster)

			'''Genotype Refinement'''
			* Update beagle2Vcf.pl to use 255 for missing PL/PL3 values
			* Update vcf2Beagle and beagle2Vcf to handle biallelic indels
			** Still doesn't handle any multiallelic variants
			* Added a ldrefine test.

			'' Indel Calling'''
			* Initial version of Indel Caller
			** Still in testing phases, if you use, please provide feedback.

	== Version 1.12 (Full Release on 1/17/2014) ==		== Version 1.12 (Full Release on 1/17/2014) ==

Mktrost: /* Version 1.12 (Full Release on 1/17/2014) */

2014-01-17T17:37:32Z

Version 1.12 (Full Release on 1/17/2014)

← Older revision		Revision as of 13:37, 17 January 2014
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	* Add some Copyright information		* Add some Copyright information
	* Fix printing of a failed run's return code		* Fix printing of a failed run's return code
	* Upgrade to latest [[LibStatGen_Download#Official Releases\|libStatGen]] & [[BamUtil#Release_of_just_BamUtil_.28does_not_include_libStatGen.29\|bamUtil]]		* Upgrade to latest [[LibStatGen_Download#Official Releases\|libStatGen]] & [[BamUtil#Release_of_just_BamUtil_.28does_not_include_libStatGen.29\|bamUtil]]. See links for version details.
	** Slightly newer than 1.0.10 for both - versions on 1/17/2014.		** Slightly newer than 1.0.10 for both - versions on 1/17/2014.
	** dedup & recab now ignore Secondary reads		** dedup & recab now ignore Secondary reads
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	* samtools		* samtools
	** Update samtools index to return an error code if it fails to build the index		** Update samtools index to return an error code if it fails to build the index


	'''Aligner'''		'''Aligner'''
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	'''Genotype Refinement'''		'''Genotype Refinement'''
	* Add a default number of states to Thunder		* Add a default number of states to Thunder


	== Version 1.11 (Full Release on 9/6/2013) ==		== Version 1.11 (Full Release on 9/6/2013) ==

Mktrost at 17:37, 17 January 2014

2014-01-17T17:37:01Z

@@ Line 1: / Line 1: @@
 For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]]
 For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
 == Version 1.11 (Full Release on 9/6/2013) ==