Changes

From Genome Analysis Wiki
Jump to navigationJump to search

GotCloud: Versions (view source)

Revision as of 12:17, 14 May 2015

4,329 bytes added ,  12:17, 14 May 2015
→‎Version 1.16 (Full Release on 2/25/2015)
Line 1: Line 1: −
 
+
__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]]
    
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) ==
 +
Source can be downloaded from: https://github.com/statgen/gotcloud/releases/tag/gotcloud.1.16
 +
 +
'''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) ==
 +
 +
'''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
 +
 +
 +
== 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) ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11273...13225"

Navigation menu