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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
