gotcloud.1.17.5

General

• Rename README from .txt to .md
• Fix runcluster.pl to not unlink $qout twice
• Some basic script cleanup
• Update pipeline.pl to check for invalid TmpKeys
• Add 'gotcloud test'
• libStatGen
  • improve SamRecord error reporting

Align

• Fix undefined variable for inferred RG fields
• verifyBamID
  • Update to work with chromosome names that contain the "chr" prefix
  • Fix a miscalculated value
• bamUtil: recab:
  • Update to write .qemp file to logfile.qemp if the output is stdout (-), so nothing is written to -.qemp like it was
  • Update to apply maxQual after binning

Snpcall

• vcfPileup - update default max # reads per site from 10,000 to 255
• glfFlex - fix bug in calculating AN

Indel

• vt - handle duplicate variants in merge
• Fix tests

Beagle4

• vcfSplit4 - fix bug due to tabix showing variants that extend into the current region

gotcloud.1.17.4

Fix slurm issue

Update htslib & samtools to latest version. This fixes some of the bugs in samtools & tabix.

gotcloud.1.17.3

gotcloud.1.17.3

ERROR - does not compile

gotcloud.1.17.2

gotcloud.1.17.2

gotcloud.1.17.1

Fix glfFlex male/female bug.

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

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

gotcloud.1.15

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

gotcloud.1.14

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

gotcloud.1.13

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.