Features, versions and roadmap
Major features planned:
Features by version
Version: 4.3 (2016-09).
Version: 4.1 (2015-01).
Version: 4.0 (2014-11).
-h
Version: 4.0 (2014-07).
annotate
: Improved annotate support.
dbNsfp
: Several improvements on annotation methods.
Version: 3.6 (2013-05-23).
concordance
: Calculate concordance statistics between two VCF files (e.g. a sequencing and a chip-genotyping experiment)
vcfCheck
command (check VCF for seferal "common" problems)
Version: 3.5 (2013-03-23).
SPLICE_REGION
annotation
private
: Annotate if a variant is "private" to a familly (or cohort)
ccs
: Case / control summary statistics (of annotated files).
annotate
: Added tabix indexed files support. Automatic detection.
Version: 3.4 (2013-11-23).
Version: 3.3 (2013-06-12).
Version: 3.2 (2013-14-01).
-o gatk
)
Version: 3.1 (2012-11-02).
Version: 3.0, revision 'f' (2012-08-23).
Version: 2.1b (2012-04-26).
Version: 2.0.5 (2011-11-25).
Version: 2.0.5 (2011-11-25).
Version: 2.0.3 (2011-10-08)
Version: 2.0.2 (2011-09-09)
Version: 1.9.6 (2011-08-08)
Full name | Short name |
---|---|
Ailuropoda_melanoleuca | ailMel1.63 |
Anolis_carolinensis | AnoCar2.0.63 |
Bos_taurus | Btau_4.0.63 |
Caenorhabditis_elegans | WS220.63 |
Callithrix_jacchus | C_jacchus3.2.1.63 |
Canis_familiaris | BROADD2.63 |
Cavia_porcellus | cavPor3.63 |
Choloepus_hoffmanni | choHof1.63 |
Ciona_intestinalis | JGI2.63 |
Ciona_savignyi | CSAV2.0.63 |
Danio_rerio | Zv9.63 |
Dasypus_novemcinctus | dasNov2.63 |
Dipodomys_ordii | dipOrd1.63 |
Drosophila_melanogaster | BDGP5.25.63 |
Echinops_telfairi | TENREC.63 |
Equus_caballus | EquCab2.63 |
Erinaceus_europaeus | HEDGEHOG.63 |
Felis_catus | CAT.63 |
Gallus_gallus | WASHUC2.63 |
Gasterosteus_aculeatus | BROADS1.63 |
Gorilla_gorilla | gorGor3.63 |
Homo_sapiens | GRCh37.63 |
Loxodonta_africana | loxAfr3.63 |
Macaca_mulatta | MMUL_1.63 |
Macropus_eugenii | Meug_1.0.63 |
Meleagris_gallopavo | UMD2.63 |
Microcebus_murinus | micMur1.63 |
Monodelphis_domestica | BROADO5.63 |
Mus_musculus | NCBIM37.63 |
Myotis_lucifugus | Myoluc2.0.63 |
Nomascus_leucogenys | Nleu1.0.63 |
Ochotona_princeps | pika.63 |
Ornithorhynchus_anatinus | OANA5.63 |
Oryctolagus_cuniculus | oryCun2.63 |
Oryzias_latipes | MEDAKA1.63 |
Otolemur_garnettii | BUSHBABY1.63 |
Pan_troglodytes | CHIMP2.1.63 |
Pongo_abelii | PPYG2.63 |
Procavia_capensis | proCap1.63 |
Pteropus_vampyrus | pteVam1.63 |
Rattus_norvegicus | RGSC3.4.63 |
Saccharomyces_cerevisiae | EF3.63 |
Sorex_araneus | COMMON_SHREW1.63 |
Spermophilus_tridecemlineatus | SQUIRREL.63 |
Sus_scrofa | Sscrofa9.63 |
Taeniopygia_guttata | taeGut3.2.4.63 |
Takifugu_rubripes | FUGU4.63 |
Tarsius_syrichta | tarSyr1.63 |
Tetraodon_nigroviridis | TETRAODON8.63 |
Tupaia_belangeri | TREESHREW.63 |
Tursiops_truncatus | turTru1.63 |
Vicugna_pacos | vicPac1.63 |
Xenopus_tropicalis | JGI_4.2.63 |
Version: 1.9.5 (2011-03-10)
Version: 1.9 (2011-03-10)
Features recently added:ailmel1.61, anoCar2.0.61, btau4.0.61, bushBaby1.61, calJac3.2.1.61, canFam2.61, cat1.61, cavPor3.61, ce.WS220.61, chimp2.1.61, choHof1.61, cInt2.61, cSav2.0.61, danRer9.61, dasNov2.61, dipOrd1.61, dm5.25.61, equCab2.61, eriEur1.61, fugu4.61, gacu1.61, ggallus2.61, gorGor3.61, hg37.61, loxAfr3.61, medaka1.61, meug1.0.61, micMur1.61, mm37.61, mmul1.61, monDom5.61, myoLuc1.61, oana5.61, ochPri2.61, oryCun2.61, ppyg2.61, proCap1.61, pteVam1.61, rat3.4.61, sacCer2.61, sorAra1.61, speTri1.61, sScrofa9.61, taeGut3.2.4.61, tarSyr1.61, tenrec1.61, tetraodon8.61, tupBel1.61, turkey.UMD2.61, turTru1.61, vicPac1.61, xtrop4.1.61
java -jar snpEff.jar dump genome_version
java -jar snpEff.jar cds genome_version cds.fasta
Older features
ailMel1.60, amel2, anoCar1.0.60, btau4.0.59, btau4.0.60, bushBaby1.60, calJac3.2.1.60, canFam2.59, canFam2.60, cat1.60, cavPor3.60, ce6, ce.WS210.60, chimp2.1.59, chimp2.1.60, choHof1.60, cInt2.60, cSav2.0.60, danRer6, danRer8.59, danRer9.60, dasNov2.60, dipOrd1.60, dm3, dm5.12, dm5.22, dm5.25.59, dm5.25.60, dm5.30, dm5.31, equCab2.60, eriEur1.60, fugu4.60, gacu1.60, ggallus2.59, ggallus2.60, gorGor3.60, hg37, hg37.59, hg37.60, loxAfr3.60, medaka1.60, meug1.0.60, micMur1.60, mm37, mm37.59, mm37.60, mmul1.60, monDom5.60, myoLuc1.60, oana5.60, ochPri2.60, oryCun2.60, ppyg2.60, proCap1.60, pteVam1.60, rat3.4.59, rat3.4.60, sacCer2, sacCer2.59, sacCer2.60, SIVmac239, sorAra1.60, speTri1.60, sScrofa9.60, taeGut3.2.4.60, tarSyr1.60, tenrec1.60, testCase, tetraodon8.60, tupBel1.60, turTru1.60, vicPac1.60, xtrop4.1.60