New Version of GotCloud (1.15) is now available

[Mary Kate Wing]

A new release of gotcloud, 1.15, is now available.  

Reminder, there is also a wiki page that describes the changes in each version:

http://genome.sph.umich.edu/wiki/GotCloud:_Versions

I have copied below the information on changes for this version.

There is also a wiki page with FAQ and issues/resolutions for specific versions:

http://genome.sph.umich.edu/wiki/GotCloud:_FAQs#Version_Problems

I am continually updating GotCloud based on User Suggestions.  So if you notice something, let me know and I will try to get it fixed.

The updates in this version are described below.

Please let me know if you have any questions.

The latest development version is always available at: https://github.com/statgen/gotcloud

Mary Kate Wing

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