What's new in snpEff 4.1k
Sep 14, 2015
- This version implements the new VCF annotation standard 'ANN' field.
New in snpEff 4.1c (Mar 31, 2015)
- This version implements the new VCF annotation standard 'ANN' field.
New in snpEff 4.1b (Feb 14, 2015)
- This version implements the new VCF annotation standard 'ANN' field.
New in snpEff 4.1 (Jan 15, 2015)
- 'ANN': New annotation standard
- Use '-formatEff' for old style 'EFF' field
- Robust HGVS notations
- Most 3'prime annotation (HGVS compatibility)
- SnpSift 'filter': More generic expressions
New in snpEff 4.0 (Aug 27, 2014)
- Major improvements and support for standards:
- HGVS notations
- Sequence Ontology terms
- Easier to use
- SnpEff downloads databases automatically
- Automatic third party databases downloads
- Support for GRCh38
- Support for Ebola Zaire Virus (2014 West Africa outbreak)
New in snpEff 3.6 (Apr 22, 2014)
- Several improvement and bug fixes:
- Sequence Ontology
- HGSV
- SnpSift dbNSFP
- SnpSift extractField
New in snpEff 3.5 (Mar 13, 2014)
- Improvements in Sequence Ontology
- SnpSift dbNSFP: Tabix indexed files
- Galaxy support: Improvements and bug fixes
- Project source moved to GitHub
- Bug fixes: Indels
- Support for large chromosomal deletions
New in snpEff 3.4 (Mar 13, 2014)
- Automatic database download ("-download" option)
- Cancer samples: can be defined using a TXT file instead of VCF header.
- Improved GenBank
- Extended cofiguration options
- Better frame handling for GTF/GFF files
- Improvements in HGSV notation
- Galaxy support: Improvements and bug fixes
- SnpSift: Better support for dbNSFP (v2.1)
New in snpEff 3.3 (Jun 13, 2013)
- Over 8,500 genomes supported.
- All ENSEMBL (version 18) : Bacteria, Fungi, Metazoa, Plants and Protist genomes added.
- NextProt annotaions added
- Motif annotations support added
- SnpSift: GeneSet annotations
- SnpEff count: Genomic region statistics counting reads, variants, intervals, etc.
New in snpEff 3.2 Dev (Apr 30, 2013)
- GATK compatibile (-o gatk)
- Cancer variants analysis
- HGSV notations support
- Loss of function tag
- Nonsense-mediated decay effect
- SnpSift: PhastCons annotations
New in snpEff 3.0 (Jul 30, 2012)
- Maven project, created by Louis Letourneau.
- Project source code changed to SVN (Louis Letourneau).
- Databases will be 'backwards compatible' from now on.
- New format for VCF files: added CDS length in amino acid (AA_LEN field).
- Canonical transcript filter (command line option "-canon").
- Improved GenBank parsing.
- SnpSift 'dbnsfp': Annotate using dbNSFP (Louis Letourneau).
- SnpSift 'gwasCat': Added GWA catalog annotations.
- SnpSift 'extractFields': extract fields to TXT files (tab separated)
- SnpSift 'sift': Annotate using SIFT database.
- SnpSift 'Annotate' and 'AnnMem': Now support to add all fields in a VCF file for annotations.