GotCloud: Versions

For information on installing the releases, see: Install GotCloud Software

For information on issues/resolutions for specific versions, see: 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: hs37d5-db142 (ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz)
• Upgrade perl scripts to use /usr/bin/env perl instead of /usr/bin/perl 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 bwa mem
  • you can still use bwa aln (the previous default) by adding the following setting to your configuration file:

    MAP_TYPE = BWA

• Upgrade to bwa version 0.7.12
• No longer call verifyBamID with the --verbose 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)

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)

General

• GotCloud now works when installed in a bin/ directory.
• Add tabix source and build & bgzip build
• Add some Copyright information
• Fix printing of a failed run's return code
• Upgrade to latest libStatGen & bamUtil. See links for version details.
  • Slightly newer than 1.0.10 for both - versions on 1/17/2014.
  • dedup & recab now ignore Secondary reads
  • mergeBam ignores PI header field when merging
  • Add PhoneHome - gotCloud applies a PhoneHome thinning (BAMUTIL_THINNING) defaulted to 10 (10% of the time bamUtil does PhoneHome)
• Upgrade QPLOT to ignore secondary reads
• samtools
  • Update samtools index to return an error code if it fails to build the index

Aligner

• Updgrade BWA
  • BWA_MEM is now an option
• Write timestamps to Makefile log as steps start & complete
• Remove tmp files as gotCloud goes, rather than at the end.
• Deprecate RUN_QPLOT & RUN_VERIFY_BAM_ID
  • Now the steps to run are specified in configuration.
• Mosaik
  • Upgrade to version from Oct 29, 2013
  • Add premo for pre-Mosaik processing

Variant Calling

• Update to properly handle empty VCFs
• Run make with -k option to run as much as possible after a failure.
• Update to allow steps to be dependent on BAMs (BAM_DEPEND) so they will rerun if a BAM has a newer timestamp.
• Input Validation
  • Check that BAMs exist & are not empty prior to running steps that require BAMs.
  • Check that filters min/maxDP are numbers, not fractions.
• GlfMultiples
  • update to use DP instead of GD and fix PL description in format field header
  • add region option
• samtools-hybrid
  • fail on missing BGZF EOF indicator

Genotype Refinement

• Add a default number of states to Thunder

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

Aligner

• Remove an extra space from the Makefile for the dedup command.
• Brought in latest bwa source, but it is not yet being used.

Variant Calling

• Rename OUT_PREFIX to MAKE_BASE_NAME to specify the base filename for snpcall, ldrefine (beagle & thunder), & vc Makefiles. The typeOfRun.Makefile is appended to MAKE_BASE_NAME.
  • These Makefiles all used to have the same name and would overwrite each other
  • --makebasename/--make_basename/--make_base_name can be specified on the command-line
  • Default value for MAKE_BASE_NAME is umake
    • snpcall is now: $(MAKE_BASE_NAME).snpcall.Makefile (default umake.snpcall.Makefile)
    • ldrefine beagle step is now: $(MAKE_BASE_NAME).beagle.Makefile (default umake.beagle.Makefile)
    • ldrefine thunder step is now: $(MAKE_BASE_NAME).thunder.Makefile (default umake.thunder.Makefile)
    • vc is now: $(MAKE_BASE_NAME).vc.Makefile (default umake.vc.Makefile)
• Added gotcloud beagle and gotcloud thunder commands so that beagle/thunder can be called independently rather than just through ldrefine.
• Add command-line options to gotcloud vc for running just certain steps rather than having to set RUN...=true in the configuration
  • More than one --commandToRun can be specified at once
  • New commands-line options:
    • --index (or RUN_INDEX = true in the configuration file)
    • --pileup (or RUN_PILEUP = true in the configuration file)
    • --glfMultiples (or RUN_GLFMULTIPLES = true in the configuration file)
    • --vcfPileup (or RUN_VCFPILEUP = true in the configuration file)
    • --filter (or RUN_FILTER = true in the configuration file)
    • --svm (or RUN_SVM = true in the configuration file)
    • --split (or RUN_SPLIT = true in the configuration file)
• Cleaned up the snpcall Makefile entries for pileup. It used to print targets/commands that were never executed. These unused targets have now been removed

Aligner & Variant Calling

• Remove trailing spaces from configuration values
• Add MAKE_OPTS configuration value that allows users to add Makefile options to the make calls that run the pipelines.
• Update gccalcstorage for better estimates and to have option to print estimates from a starting size rather than from actually input files

Version 1.10 (Full Release on 8/22/2013)

Aligner

• Update gccalcstorage for better align estimates

Variant Calling

• Add additional comments to umake.pl
• Update vcf-summary to print the skipped counts
• Add option to specify the REF_FAI file used by the umake (gotcloud) script for determining CHRs and their lengths.

Aligner & Variant Calling

• Only print Configuration settings to a file if the file doesn't exist

Version 1.09a (Full Release on 8/08/2013)

Aligner

• Fix relative paths
• Upgrade to newest samtools (and add source)
• Update gcrunsummary.pl - summary stats for the run.
• Upgrade to newer Mosaik

Variant Calling

• Fix minNS filter for odd number of samples. It used to give a fraction and then would be ignored.

Aligner & Variant Calling

• Cleanup phonehome script
• Cleanup gotcloud script and add ability to run perf/audria for dev purposes.

Version 1.08 (Full Release on 7/31/2013)

Aligner

• no aligner only changes

Variant Calling

• Add the ability to copy a glf to a different directory prior to running glfExtract or glfMultiples
• Remove chromosome Y from the default CHRS. Also allow CHRS to be set on the commandline via a comma separated list specified in --chrs
• Update glfMerge to skip glf files that only have a header.
• Change default FILTER_MAX_SAMPLE_DP to 1000 (from 20)
• Some SVM updates
• Added the vc option to gotcloud which uses the RUN_...settings to decide which steps to use.

Aligner & Variant Calling

• Fix bug in Conf.pm that caused a failure in some versions of perl
• Add the ability to set the GOTCLOUD_ROOT so you can test with an alternate align.pl/umake.pl script and still be able to access everything else from the standard gotcloud path.
• Cleanup the perldoc for align/snpcall
• Output all configuration settings into a file when running.
• Upgrade to most current libStatGen
• Compile as optimized

Version 1.07 (Full Release on 7/3/2013)

Aligner

• DEPRECATED configuration settings:
  • 'BWA_MAX_MEM' is now 'SORT_MAX_MEM'
  • 'VERIFY_BAM_ID_OPTIONS' is now 'verifyBamID_USER_PARAMS'
• ALN_TMP now defaults to $(TMP_DIR)/alignment.aln rather than $(TMP_DIR)/alignment.bwa
• Upgrade to latest QPLOT
  • GC Content file has been renamed to have the extension: .winsize100.gc
• Automatically generates the bam index file if BAM_INDEX is specified
• Run DEDUP & RECAB as 1 step instead of 2
• Update dedup, recab, qplot, & verifyBamID steps to be specified via configuration
  • Easier to insert steps between/before/after these
  • Use PER_MERGE_STEPS to disable any of these steps (see gotcloudDefaults.conf for its default setting)
    • RUN_QPLOT and RUN_VERIFY_BAM_ID are only used for validating executable/reference existence and will be deprecated completely soon
• Fixed bug where the merge failed if there was only 1 fastq pair
• Improve informational messages
• Update to BWA version 0.6.1-r104
• Bring in mergeBam updates from latest bamUtil
  • ignore PG lines with duplicate ids
• General code cleanup
• Add some Mosaik support
  • Added support to align.pl and a way to enable it, but the code doesn't compile
• Calculate approximate storage needed for GotCloud so user can have an idea what is coming
• Makefile now uses bash and pipefail to catch errors that occur within piped commands
• Removed the md5sum calculation

Variant Calling

• Update to always require REF
  • this fixes bug that ldrefine was not checking REF or adding the optional prefix to it.
• SVM - fix bug on qual check in run_libsvm.pl
• Update defaults for filtering
• Fixed bug in libVcf/VcfFile that had FamID instead of FatID
• Fixed bug in samtools-hybrid that caused it to fail when checking for BAI files if bam was elsewhere in the filename
• Fix vcfPielup to accept .bam.bai or .bai in bam index filenames.
• Fix the split logic to work if a VCF file had no PASS records

Aligner & Variant Calling

• Add checks for required executables prior to running
• Limit the number of jobs that can run locally (there is a flag to override this)
• Extract configuration routines from the 2 .pl's to a common Conf.pm
• Add FLUX support
• 1st attempt at checking for new versions
  • Doesn't quite always work yet, but shouldn't cause a problem

Version 1.06 (Full Release on 4/17/2013)

Variant Calling

• Update to always require REF
  • this fixes bug that ldrefine was not checking REF or adding the optional prefix to it.

Version 1.05 (Full Release on 4/17/2013)

Aligner & Variant Calling

• Cleanup handling of BASE_PREFIX & added REF_PREFIX.
  • Allows user to specify --base_prefix or --baseprefix on command-line
  • Now used for index files & reference files in addition to fastqs (aligner) and bams (variant calling)

Version 1.04 (Full Release on 4/16/2013)

Aligner & Variant Calling

• Update relative paths to be relative to the current working directory
  • Aligner effects:
    • INDEX_FILE as specified in the aligner configuration
    • fastq paths specified in the INDEX_FILE
  • Variant Calling effects:
  • BAM_INDEX as specified in the configuration
  • bam paths specified in the BAM_INDEX
• Add getAbsPath() method for determining the absolute path with the additional capability of prepending an optional PREFIX (as specified in configuration) to the directory:
  • BASE_PREFIX
  • FASTQ_PREFIX (for aligner reading the fastq index file)
    • renamed from FASTQ/FASTQ_REF
  • BAM_PREFIX (for variant calling reading bam index file)
• Improve Error detection
  • With --test option, check that the testdir exists before running the test

Cluster Support

• Update the mosix option to run mosbatch instead of mosrun
• Only attempt to "fix" the CWD for mosix/mosbatch
  • Remove the warning if this "fix" fails
  • This "fix" is specific for running at UM, but should not cause a failure when running elsewhere

Includes all updates from previous Internal Only Releases.

Version 1.03a6 (Internal Only Release on 4/10/2013)

• Cleanup the cluster support code
  • Also add support for fixing the problem with UMich directories when using Mosix
• Update the default Reference directory to be as expected for UM
• Variant Calling changes:
  • SVM
    • Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing)
  • Cleanup some of the Makefile dependencies to depend on files rather than phony targets (this prevents it from always rerunning those steps)

Version 1.03a5 (Internal Only Release on 4/5/2013)

• Add pre-checks for required files & reference files prior to running
• Add checks for deprecated configuration settings
• Merge aligner & variant calling default configurations into a single file (bin/gotcloudDefaults.conf)
• Aligner
  • Update to put actual values into the Makefile recipes rather than using variables
• Variant Calling
  • Fix vcf-summary to handle chromosomes that have string names (like X,Y)

Version 1.03a4 (Internal Only Release on 4/2/2013)

• Variant Calling:
  • Update to by default run as local
  • Target Loci file updates:
    • When WRITE_TARGET_LOCI is set to true: only generate the .loci file if the specified bed is newer than the loci file
    • When WRITE_TARGET_LOCI is set to ALWAYS, generate the .loci file regardless of the timestamps
  • Only create the glf index file for a region if it does not exist or is older than the bam index file

Version 1.03a3 (Internal Only Release on 3/29/2013)

• Attempted to Fix bug that it wasn't properly running batching
  • This version was not good (fixed in 1.034a.

Version 1.03a2 (Internal Only Release on 3/27/2013)

• Add the qplot source code

Version 1.03a1 (Internal Only Release on 3/26/2013)

• Variant Calling
  • Add FILTER_MIN_NS to add the option of filtering based on the number of samples
  • Add FILTER_ADDITIONAL to add the option of adding additional filters.

Version 1.03a (Full Release on 3/22/2013)

• Cleanup README & INSTALL instructions
• Variant Calling
  • Fix dependency bug/error in SVM
  • Fix commands that run locally to check for pipe failures
  • Improve file open error detection in SVM logic
• Add option to obtain the version number

Version 1.03 (Full Release on 3/15/2013)

• Add SVM Filtering
  • there was a bug in this, please do not use this version.
  • Version 1.03a fixes this bug.

Version 1.02 (Full Release on 3/13/2013)

• Cleanup cluster scripts
• Rename alinger to align.pl & umake to snp
• Add VerifyBamID source
• MANY Updates, please use a newer version.