New version: 2.0.4.rc1 (2011-11-15). Release Candidate 1http://snpeff.sourceforge.net/
Take a look at all the new features added
- Database download command, e.g. "java -jar snpEff.jar download GRCH37.64"
- RefSeq annotations support added.
- Rogue transcript filter: By default SnpEff filters out some suspicious transcripts from annotations databases. This should improve false positive rates.
- Amino acid changes in HGVS style (VCF output)
- SnpSift: Added 'intIdx', looks for intervals using indexing and memory mapped I/O on the VCF file. Works really fast! Designed to extract a small number of intervals from huge VCF files.
- Optimized parsing for VCF files with large number of samples (genotypes).
- Option to suppress summary calculation ('-noStats'), can speed up processing considerably in some cases.
- Option '-onlyCoding' is set to 'auto' to reduce number of false positives (see next).
- Option '-onlyCoding' can be assigne a value: If value is 'true', report only 'protein_coding' transcripts as proteing coding changes. If 'false', report all transcript as if they were conding. Default: Auto, i.e. if transcripts any marked as 'protein_coding' the set it to 'true', if no transcripts are marked as 'protein_coding' then set it to 'false'.
- Added BED output format. This is usefull to annotate the output of a Chip-Seq experiment (e.g. after performing peak calling with MACS, you want to know where the peaks hit).