vcfhacks v0.2.2

v.0.2.2a

submodule update

vcfhacks v0.2.1

Release Information

This release fixes some issues with the previous (v0.2.0) release and adds a small number of new features.

Changes

• Fixes an issue which would prevent any scripts running with certain versions of perl
• Added addFilterField.pl script for quickly tagging all variants in a VCF with a FILTER annotation
• Fixed an issue with annovcfToSimple.pl not outputting the advertised default fields.
• Prevented getVariantsByLocation.pl or geneAnnotator.pl from making too many REST queries in too short a time
• Added --vcf_af and --min_af_counts options to findBiallelic.pl to allow filtering on alleles based on frequency within the input VCF
• Added option to filterOnSample.pl to allow filtering on allele frequency only when a minimum number of alleles have been called (--min_alleles_for_freq)
• filterOnSample.pl can now be run to filter on allele frequency without specifying --samples, --reject or --reject_except options
• scripts that read a VCF index will now check age of index and warn if the index is older than the VCF
• added a temporary fix for OMIM's new download arrangements to geneAnnotator.pl
• rankOnCaddScore.pl now has --keep_unscored option for not filtering variants without a CADD score when using the --filter option

version 0.2.0

Release Information

This is a significant update with many changes and fixes. Some of the more important changes include handling of the new '*' alleles produced by variant callers, better compatibility with VCFs produced by freebayes, ensemblGeneAnnotator.pl (now named geneAnnotator.pl) adds BIOGRID interactants and use of phase information by findBiallelic.pl.

Old ensemblGeneAnnotator databases will no longer be compatible with geneAnnotator.pl, which now looks in the 'data/geneAnnotatorDb' subdirectory by default or database files. An up to date version of this database comes bundled with this release or can be downloaded separately from this release if cloning the git repository instead.

annotateSnps.pl can use the ClinVar TSV file from the MacArthur lab (https://github.com/macarthur-lab/clinvar) for better dissemination of previously reported pathogenic variants. annotateSnps.pl, filterOnEvsMaf.pl and filterVcfOnVcf.pl all write frequency data to INFO fields in their output files which can subsequently be read by findBiallelic.pl and getFunctionalVariants.pl for filtering on allele frequency at the allele (rather than variant) level.

Bioperl modules required for geneAnnotatorDb updates are now provided in the 'lib' subdirectory (meaning installation of the full Bioperl distribution is no longer required) as well as a patched version of the Tabix perl module to make installation more simple.

Changes

• ensemblGeneAnnotator.pl is now renamed geneAnnotator.pl.
• geneAnnotator.pl can annotate snpEff annotated VCF files annotates using the newer 'ANN=' style annotations in addition to VEP annotated VCFs.
• geneAnnotator.pl now annotates BIOGRID interactants.
• geneAnnotator.pl will attempt to retrieve Entrez gene IDs remotely if they are not in the database.
• geneAnnotator.pl can also be used to work on a list of genes, not just on VCFs.
• getFunctionalVariants.pl and findBiallelic.pl replace the VEP and SnpEff specific scripts and can be used on either VEP or SnpEff annotated files (only the newer 'ANN' style SnpEff annotations are supported).
• in the interest of speed, findBiallelic.pl checks that input is sorted on-the-fly rather than doing a pass of the whole file before running.
• findBiallelic.pl now feature the option to look at variants compatible with X-linked recessive inheritance as well/instead of autosomal recessive inheritance.
• findBiallelic.pl will read phase information (PID and PGT) from GATK if present and not consider variants in cis as potential compound hets.
• findBiallelic.pl and getFunctionalVariants.pl can use Cadd score annotations from rankOnCaddScore.pl to filter alleles.
• findBiallelic.pl and getFunctionalVariants.pl can use custom allele frequency annotations for filtering alleles.
• findBiallelic.pl and getFunctionalVariants.pl can now filter genotypes using genotype PL annotations.
• getVariantsByLocation.pl can retrieve variants that overlap given genes.
• filterVcfOnVcf.pl can now filter using population specific allele frequency fields, particularly in the case of ExAC VCFs.
• filterVcfOnVcf.pl can be used to add custom allele frequency annotations.
• Parsing of VEP alleles is improved, which should prevent some 'undefined variable' errors in scripts that parse VEP annotations.
• Compatibility with VCFs produced by freebayes is improved, where allele depths will be calculated from 'AO' and 'RO' genotype fields in the absence of 'AD' fields.
• VEP's (rather vague) 'protein_altering_variant' class is now included by default as a 'functional' variant in relevant scripts.
• filterOnSample.pl now features the option to only consider samples with a minimum read depth at a variant site.
• rankOnCaddScore.pl can now take a directory as an argument in order to find any .(b)gz files contained to use for CADD annotations.
• scripts handle the new '*' allele codes appropriately.
• getHetVariants.pl features the option to specify minimum and maximum allele balances for a call to be considered heterozygous.
• added checkInheritance.pl, renameSamples.pl and removeVariantInfoFields.pl scripts.
• fixed 'not numeric value' errors from no-calls when processing genotype qualities.
• fixed an issue when using a custom set of VEP fields in annovcfToSimple.pl where the consequence or allele fields would not be retrieved.

vcfhacks v.0.1.17

vcfhacks v0.1.17

This is a minor update that fixes a couple of bugs. For the latest ensemblGeneAnnotator database and separate VEP plugins tarball see the v0.1.16 release. For details of the difference between the scripts or binary releases see the readme displayed on the main project page.

Release Information

-fixed bug with handling of VEP output where indels alleles are called at the same site as SNV/MNV alleles.

-improved efficiency of sorting operations and fixed bug with Sort::External methods

-fixed an error with the --gene_id_mode option in getFunctionalVariantsSnpEff.pl

vcfhacks v.0.1.16

vcfhacks v0.1.16

As well as the scripts precompiled executable versions of the scripts are now available for 64-bit Linux and Mac OS X. These binaries can be run without the need for installing perl modules on your machine.

If you prefer to download the scripts themselves download vcfhacks_scripts-0.1.16.zip. For the binary executables download vcfhacks_binaries-linux_0.1.16.tar.bz2 or vcfhacks_binaries-macosx_0.1.16.tar.bz2 depending on your OS. The two VEP plugins (SpliceConsensus.pm and SpliceConsensusFilter.pm) are available in a separate tarball for those that prefer to download the binary release.

Release Information

Several bugfixes and improvements:

-ensemblGeneAnnotator.pl now supports annotating RefSeq/Entrez IDs (i.e. if VEP was run using --refseq or --merged database options)

-ensemblGeneAnnotator.pl now supports use of SnpEff annotations (as long as -geneId flag was used when running snpEff)

-fixed an issue where files might be incorrectly interpreted as being bgzip compressed

-fixed an issue with filterVcfOnVcf.pl where a rogue progress message might print to STDOUT (and therefore appear in output if using > to redirect output rather than using -o option)

-fixed an issue with annovcfToSimple.pl where an extra column was added when using --summarise option without --contains_variant option

-ensured that INFO lines generated by annotateSnps.pl conform to VCF spec (i.e. GATK does not object to these lines anymore)

-additional modules are now moved into the lib subdirectory for tidyness

-URL for the github examples markdown file provided in readme

-progress bar in ensemblGeneAnnotator.pl is now optional with the --progress option

-updated pre-built ensemblGeneAnnotator database and made available as part of this release on github.

v.0.1.15

First release since moving to github. Previous releases at https://sourceforge.net/projects/vcfhacks/

See readme.md file for more details.