1.  Version 2.7.0 (Released on Jan 20, 2016)

MAJOR NEW FEATURES:

  • Normalize variants using reference sequence information before importing variants.
  • New file format for spec file of variant pipeline tools.
  • Support arbitrary reference genome.

BUG FIXES:

  • Fix importing wildtype genotypes in some cases.

2.  Version 2.6.1 (Released on Jan 15, 2015)

  • Fix a few small bugs introduced in 2.6.0.
  • Fix compatibility issues with Python 3.

3.  Version 2.6.0 (Released on Dec 15, 2014)

NEW FEATURES:

  • Major cleanup of the pipeline code (vtools execute and vtools simulate), especially for the pipeline action interface.
  • Add command vtools show actions and vtools show action ACTION.
  • Select annotation databases automatically (the latest version for project annotation database) for command vtools use annoDB when no version information is given.

4.  Version 2.5.1 (Released on Nov 10, 2014)

BUG FIX:

  • Nov 1st: Fix the handling of runtime option temp_dir

NEW FEATURES:

  • Nov 3rd: Add function in_table.

5.  Version 2.5.0 (Release on Oct 15, 2014)

MAJOR NEW FEATURE:

  • Oct 2nd: Implement a mirrored file distribution system so that users can download resources from multiple servers.
  • Oct 5th: Add site_options.py to allow system administrator to set up site-wide resource directory for variant tools users.

NEW FEATURES:

  • Oct 5th: Add md5 signature of database files to .ann files and re-decompress .DB.gz files if the decompressed .DB files are corrupted.

6.  Version 2.4.1 ((Released on August 20, 2014))

BUG FIX:

  • Fix a python2/3 compatibility bug that prevents vtools from working properly under python2.

7.  Version 2.4.0 (Released on August 15, 2014)

MAJOR NEW FEATURE:

  • June 10: Variant Simulation Tools is introduced to simulate genetic samples with common and rare variants.

NEW FEATURE:

  • Mar 13: Allow the specification of a header using option --header for command vtools phenotype --from_file.
  • May 15: Progress bar for saving and loading snapshots.
  • May 15: Use faster compression for local compressed snapshots.
  • May 20: Add option --translate to command to output protein sequence of genes in specified region.
  • Jun 5: Allow the execution of many information-based commands such as vtools show annotations without a project.
  • Jun 26: New features in pipeline allows definitions of multiple steps using one section.
  • July 5th: Add option --build to command vtools init

BUGS:

  • June 5: Allow the use of function genotype() when one or more samples do not have genotype.

8.  Version 2.3.0 (Released on Feb 27, 2014)

BUGS:

  • Jan 26: Fix a bug with pipeline functor DecompressFiles when the input tar file contains directories.
  • Feb 22: Fix a bug with wildcard match with table names having special characters such as ( or ).

NEW FEATURE:

  • Feb 19: Add option --expression to command vtools compare.
  • Feb 20: Add pipelines filtering to identify recessive and de novo mutations in families with unaffected parents and an affected offspring.
  • Feb 20: Allow the use of snapshot files (or name of online snapshot name) as --child or --parent in command vtools init.
  • Feb 22: Keep a copy of original variant tables when merging projects.

9.  Version 2.2.0 (Released on Jan 16, 2014)

MAJOR NEW FEATURES:

  • Jan 12, 2014: Add parameters type, show_seq, delimiter, limit and strand to track() function for bam tracks.
  • Dec 4nd: Add command vtools admin --validate_sex to check sample sex using genotypes on sex chromosomes.
  • Dec 3nd: Add command vtools_report inbreeding_coefficient to compute individual level inbreeding coefficient, the F-statistic.
  • Nov 15: Add sub-commands plot_fields, plot_geno_fields and plot_pheno_fields to vtools_report. These commands generate summary plots for specified variant/genotype/sample information.
  • Dec 2nd: Add special function maf() to command vtools update --from_stat to calculate minor allele frequency.

NEW FEATURES:

  • Jan 16, 2014: Update gwas catalogue annotation database.
  • Jan 16, 2014: Add annotation databases for Database of Genomic Variation (DGV).
  • Jan 10, 2014: Add population-specific hapmap frequency annotations.
  • Jan 6th, 2014: Add pipeline import_vcf to import all variant and genotype info from vcf file.
  • Jan 6th, 2014: Add pipeline anno_utils.annFileFromVcf to make it easier to create an annotation database from vcf files.
  • Nov 22: Add an annotation database for expanded exome regions of the Illumina Nextera Rapid Capture Expanded Exome Enrichment Kits.
  • Nov 29: Add KING pipeline to perform global ancestry and kinship analysis.

BUG FIXES:

  • Jan 8: Do not abort vtools remove genotypes if genotypes from one of the samples fail to remove.
  • Jan 4: Fix a multi-processing bug with functor FieldFromDb.
  • Dec 2: Fix a regression bug for online vcf track.
  • Nov 14: Fix the use of annotation field if the annotation database has the same name of a variant table.
  • Nov 18: Fix import PLINK format to allow for arbitrary coding for unknown "sex" status in fam file.
  • Nov 20: Properly handle meta analysis input with trailing white space in column names.
  • Nov 27: Properly handle missing data in external weight for $vtools associate command.

10.  Version 2.1.0 (Released on Nov. 6th)

MAJOR NEW FEATURES:

  • Nov 4: Add option --as to command vtools use, which allows the use of multiple versions of the same annotation databases.
  • Oct 25: Add SQL function samples() to output samples that contain the variants.
  • Oct 21: Add SQL function genotype() to output genotypes that contains the variants.

NEW FEATURES:

  • Nov 6: Add option all=1 to parameter field of track() function and deprecate the third option.
  • Oct 30: Add pipelines ANNOVAR and snpEff to facilitate the use of ANNOVAR and snpEff to get variant effect estimate.
  • Oct 25: Allow the use of wildcast characters in the first (filename) parameter of the track function.
  • Oct 22: Add descriptions to fields added to the project using command vtools update --from_stat and vtools update --set.
  • Oct 22: Add option --delimiter to command vtools associate.
  • Oct 17: Handle missing phenotypes more cleverly.
  • Oct 10: Allow the output read tags and use of tags for read filtering in the track function of BAM tracks.

BUGS:

  • Oct 24: Fix a bug that caused misalignment of reads in the output of BAM track when the reads are clipped in CIGAR string.
  • Oct 11: Fix a bug related to exporting a large number of samples (> 60) in vcf format.

11.  Version 2.0.1 (Released on Oct 7th, 2013)

NEW FEATURES:

  • Oct 5: Update dbNSFP to version 2.1.
  • Oct 3: align columns of output of command vtools output and vtools show genotypes using variable spaces.
  • Sep 23: Save ${local_resource} in annoDB to increase portability of projects.
  • Sep 2: Expand command vtool compare to compare location and genotypes as well.

BUGS:

  • Oct 5: Fix the vcf exporter for multiple variants at the same location.
  • Oct 4: Fix indel track mismatch for vcf track files because position adjustment for indels.
  • Oct 2: Fix a deadlock bug for flag info when using vcf track.
  • Sep 18: Fix a bug in vtools admin --merge_samples.
  • Sep 23: Fix a crash caused by unrecognized chromosome name or out of range positions in function ref_sequence.
  • Sep 25: Fix a bug related to the use of arbitrary table name in command vtools update.

12.  Version 2.0.0 (Released on Aug. 27, 2013)

MAJOR NEW FEATURE:

  • Aug. 15: Add function track to annotate variants using vcf, bigWig and bigBed tracks.
  • Jun. 28: Add command vtools execute pipeline to execute variant tools pipelines.
  • July 13: Add option --all to vtools output, vtools select --output and vtools export to remove duplicated lines without sorting output.

NEW FEATURE:

  • Aug. 14: Add item fmt to field definitions used to output fields.
  • Aug. 14: Add functors InfoFormatter and FlagFormatter to output fields in vcf format.
  • Aug. 13: Add SQL functions ref_sequence.
  • Aug. 12: Add runtime option check_update.
  • Jul. 11: Allow .ann files to use preprocessor to process files before importing.
  • Jul. 11: Add a preprocessor Dos2Unix to convert files with \r as newline character to unix format.
  • Jul. 10: Change the output of vtools show table TABLE to make it more informative.
  • Jul. 5: Allow exporting genotypes in format csv.
  • Jun. 29: Add a feature that allows vtools admin --rename_samples COND NAME1 NAME2 to rename samples by replacing the first incidence of NAME1 in selected samples to NAME2.
  • Jun. 29: Add annotation database genomicSuperDups and phast cons elements
  • May 24: Check duplicate genotypes after samples are imported.
  • Jun. 25: Allow importing csv files for command vtools phenotype --from_file.
  • Jun. 25: Add command vtools show phenotypes P1 P2.
  • Jun. 25: Allow command vtools show samples to show a selected list of samples.

13.  Version 1.0.6 (Released on May 16th, 2013)

NEW FEATURE:

  • May 16: Allow the merge of projects with different phenotypes.
  • May 14: Adding a few fields to vcf.fmt for Illumina data.
  • May 6: Extend vtools update --from_file to update genotype info from non-original input file, and without genotype.
  • Apr. 15: Allow the use of wildcard characters in command vtools compare
  • Apr. 22: Allow the merge of project with different variant tables and fields

BUG FIXES:

  • May 16: Allow the use of non-ascii table name in commands vtools export and output/
  • May 15: Remove statistics missing from vtools phenotype because it is not meaningful.
  • May 10: Fix runtime variable local_resource
  • May 10: Fix importing data in binary plink format.

14.  Version 1.0.5 (Released on Mar. 20, 2013)

NEW FEATURES:

  • March, 2013: Allow the use of arbitrary characters in name of variant tables.
  • March, 2013: Add command vtools admin --update_resource to download all relevant resources.
  • March 18, 2013: Add command vtools_report sequence to output nucleotide sequence at specified chromosome region.

BUG FIXES:

  • Feb 26, Fix a bug with command vtools select --samples when there are more than 50 specified samples.

15.  Version 1.0.4 (Released on Feb 22, 2013)

NEW FEATURES:

  • Oct 20, 2012: Allow users to list and download online snapshots, which are used for training and documentation purposes.
  • Oct 20, 2012: Use colors to differentiate debug, info, warning and error message.
  • Nov 2, 2012: Define runtime option local_resource and use resources from this directory first.
  • Nov 3, 2012: Add command vtools admin --validate_build.

16.  Version 1.0.3 (Released on Sep 21, 2012)

NEW FEATURES:

  • Jul 11, 2012: Add command vtools admin --reset_runtime_option and vtools show runtime_options.
  • Jul 4, 2012: Reorganize the association test to improve the efficiency of vtools associate.
  • Jun 16, 2012: Reorganize the import process to substantially improve the efficiency of vtools import when it is used to import files with a large number of samples.
  • Jun 15, 2012: Add command vtools admin --rename_table and vtools admin --describe_table to change the name and meta information of variant tables.
  • Jun 12, 2012: Allow a comment string when a variant table is created from command vtools select, vtools exclude, and vtools compare.
  • May 21, 2012: Add Exact Tests of Hardy-Weinberg Equilibrium and Fisher's exact test for case/ctrl associations to vtools update
  • May 12, 2012: Add command vtools admin.
  • Jan 27, 2012: Analyze project database automatically (if needed) to improve the performance of queries.
  • Feb 29, 2012: Completion of the interface of command vtools associate
  • Mar 1, 2012: add output formatting options --header, --na, --delimiter and --limit to vtools phenotype
  • Mar 5, 2012: add parameter --genotypes to command vtools init --parent. (This option was defined but not implemented).

BUGS:

  • Jan 27, 2012: Correctly handle missing data when exporting genotype in TPEF format
  • Feb 9, 2012: Allow the use of single field name (e.g. ccdsid instead of dbNSFP.ccdsid) for parameter --linked_by of command vtools use
  • Feb 17, 2012: Fix a bug with exporting deletion in vcf format, for python2 version of variant tools.

17.  Version 1.0.2 (released on Jan 24, 2012)

NEW FEATURES:

  • Jan 4, 2012: add parameter --style to format tped to allow output of genotype in numeric style
  • Jan 4, 2012: allow command vtools phenotype --from_stat to use conditions that involve variant tables in the project.
  • Jan 23, 2012: Add a new import format map. A new functor is created to retrieve reference and alternative alleles from dbSNP.

BUGS:

  • Jan 11, 2012: Fix a bug that prevents the removal of genotype in command vtools remove variant if the genotype tables are not indexed.
  • Jan 11-13, 2012: Fix the use of vtools_report under python 3.
  • Jan 17, 2012: Fix the use of annotation database when exporting in TPED format.
  • Jan 23, 2012: Remove the use of COLLATE in a query to avoid potential compatibility problems.
  • Jan 23, 2012: Fix a bug that causes duplicate output in commands vtools output and vtools export.
  • Jan 23, 2012: Fix a bug for the detection of the existence of indexes.

18.  Version 1.0.1 (released on Jan 2nd, 2012)

NEW FEATURES:

  • Nov 20, 2011: associate command can now be executed under python 3
  • Nov 27, 2011: Add entry encoding to .ann and .fmt in order to import files with non-ascii characters
  • Dec 06, 2011: Give a warning when duplicated records are outputted
  • Dec 13, 2011: Stop altering user-provided headers for command vtools output.
  • Dec 13, 2011: Add a parameter --order_by to order output from commands select, exclude and output.
  • Dec 13, 2011: Add a new format csv.fmt in order to output fields in csv format (with properly quoted fields)
  • Dec 14, 2011: Add a keyword sort_output_by to file format specification in order to sort variants by specified fields.
  • Dec 14, 2011: Allow command vtools output to read a header from standard input using option --header -.
  • Dec 15, 2011: Add parameters anno_type and linked_fields to command vtools use in order to allow the flexibility of how an annotation database it linked.
  • Dec 15, 2011: Beautify output of vtools show when there are multiple variant tables and annotation databases.
  • Dec 15, 2011: Adding a new interface for command vtools compare and allow the comparison of more than two tables, using new parameters --intersection, --difference, and --union. The old interface still exits and functional, but has been marked as deprecated.
  • Dec 28, 2011: Allow the use of wildcard characters ? and * in table names in command vtools remove tables.

DEPRECATED:

  • Dec 14, 2011: Parameter filename for command vtools export is deprecated. Using a pipe to save output to a file is recommended.
  • Dec 15, 2011: Parameter --A_and_B, --A_or_B, --A_diff_B, and --B_diff_A are deprecated. Parameters --intersection, --difference, and --union should be used instead.
  • Dec 29, 2011: Use of name 'field annotation database' instead of 'attribute annotation database' for consistency considerations. Both names are however allowed in .ann file for backward compatibility considerations.

BUGS:

  • Dec 15, 2011: Fix a bug when number of genotype is counted when one or more samples do not have genotype field GT.
  • Dec 15, 2011: Fix a bug where vtools update table --set FIELD=NULL fails because variant tools cannot determine the type of the RHS value. This should be allowed when the LHS is an existing field.
  • Jan 1, 2012: Fix vtools export --format vcf for the output of genotype when there are two different alternative alleles.

REGRESSIONS:

  • Dec 14, 2011: parameter --header of command vtools export is redesigned to work similarly to parameter --header of the vtools output command.

INTERNAL IMPROVEMENTS:

  • Nov 17, 2011: Improve efficiency of commands vtools compare by using direct SQL query in the case of --verbosity 0
  • Nov 17, 2011: Improve efficiency of vtools remove variants by creating indexes for genotype tables before removing variants.
  • Nov 25, 2011: Improve efficiency of vtools select by creating indexes of relevant fields of the annotation database.
  • Dec 28, 2011: Improve efficiency of commands vtools select for ranged based queries by creating auxiliary binning tables.