Package: jacquard
Suite of command-line tools to expedite analysis of exome variant data from
multiple patients and multiple variant callers.The official repository is at:https://github.com/umich-brcf-bioinf/JacquardUsage$ jacquard <subcommand> [options] [arguments]Subcommandstranslate:Creates new VCFs, adding a controlled vocabulary of new FORMAT tags.merge:Integrates a directory of VCFs into a single VCF.summarize:Adds new INFO fields and FORMAT tags that combine variant data from the
merged VCF.expand:Explodes a VCF file into a tab-delimited file.For help on a specific subcommand:$ jacquard <subcommand> --helpSeeReadTheDocsfor full documentation.Emailbfx-jacquard@umich.edufor support and questions.UM BRCF Bioinformatics CoreInstalling JaquardJacquard has been tested with Python 2.7 and 3.4 on Windows7, OSX, and *nix.PrerequisitesNotePip installs all required libraries; see [Installing] below.natsort (3.5.2)nosetests, testfixtures (3.0.2), and numpy (>=1.7.1) are required for running
automated testsInstallingThe easiest way to install Jacquard is through PyPI. Get pip if it’s
not available in your system:$ pip install jacquardYou can install from source from github:$ pip install git+https://github.com/umich-brcf-bioinf/JacquardIf you don’t have root permissions, you can install locally:$ pip install --user jacquardNoteYou may need to modify your path to include the Python install dir
(e.g. /Users/<username>/.local/bin)Changelog1.1.5 (10/26/2020)Adjusted Mutect translate to handle new style tumor/normal sample metaheaders.Adjusted Mutect translate to clarify supported versions of Mutect.1.1.4 (9/29/2020)Adjusted summarize to ignore phasing when creating consensus GT.Adjusted Mutect handling to correctly marked phased normal (0|0)
as non-somatic.Removed extraneous fields from JQ_VS_LOW_CONFIDENCE filter metaheader.1.1.3 (9/24/2020)Adjusted Mutect handling to accommodate either older FA or newer AF
allele frequency tags.1.1.2 (7/11/2019)Adjusted VCF handling to correctly pad optional trailing FORMAT fieldsAdjusted Mutect translation to regard PASS as somatic when FilterMutectCalls
present in metaheaders.1.1.1 (10/30/2018)Adjusted Mutect translators to:parse normal and tumor designations from SAMPLE metaheaders if availablerecognize more variations of Mutect metaheader formats1.1.0 (6/18/2018)Adjustedtranslateto correctly parse newer versions of MutectUpdated supported versions for Mutect, Strelka, VarscanFixed error in JQ_SUMMARY_DP_AVERAGE tag description1.0.0 (6/5/2018)Removed obsolete spikes directoryFixed bug inexpandwhich could overwrite fixed VCF fields (e.g. REF, ALT,
etc.) if identically named fields in INFO.Switched to semantic versioning0.42 (9/22/2015)Added docs on readthedocs.Improved workflow documentation with example dataMergewill now disambiguate tag collisions from multiple VCsTranslate/summarizenow supports GT tagsExtended precision to 4 decimal places to support analysis of gene-panels.Adjusted translate to handle empty high-confidence VarScan files.0.41 (5/7/2015)Combinedfiltercommand withmergecommandExtendedexpandto create simple metaheader glossaryAdjusted code to support Python >=2.7 or 3.xImproved checks for consistent VCF file setsFixed bug inmergethat caused error if any VCFs were unsortedFixed bug insummarizethat caused error if variant was called by subset
of callers0.31 (3/17/2015)Downgraded VCF format from 4.2 to 4.1Fixed a bug that omitted CALLERS_REPORTED_LIST summary tagSimplified summary tags; removed dependency on numpyAdjusted VarScan translation to accept a file pattern to identify
high-confidence files0.3 (3/9/2015)Replacednormalize,tagcommands withtranslate; relaxed constraints
on incoming data.RenamedconsensustosummarizeMore consistent behavior inexpandSignificantly improvedmergeperformanceAdded new summary tags:CALLERS_REPORTED_COUNTCALLERS_REPORTED_LISTSAMPLES_REPORTED_COUNTCALLERS_PASSED_COUNTCALLERS_PASSED_LISTSAMPLES_PASSED_COUNTFixed bug in how Strelka calculated AF on indelsImproved command validation and error handlingAdded project/code documentationRemoved dependencies on pandas0.21 (10/2014)Initial public releaseJacquard is written and maintained by the University of Michigan
BRCF Bioinformatic Core; individual contributors include:Jessica BeneAshwini BhasiChris GatesDivya KritiKevin MengPeter Ulintz