gotcloud.1.12: Release version 1.12

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
  • 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

gotcloud.1.11

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

gotcloud.1.10

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