Difference between revisions of "SnpEff"
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{{#if: {{#var: installation}}|==Installation== | {{#if: {{#var: installation}}|==Installation== | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
| + | |||
| + | ==Reference Databases== | ||
| + | {{:SnpEff_Databases}} | ||
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Revision as of 22:23, 14 December 2015
Description
- SnpEff
- Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
- Features
- Supports over 8,500 genomes.
- Cancer variants analysis
- GATK compatibile (-o gatk)
- HGSV notations support (clinical)
- SnpSift
- SnpSift helps filtering and manipulating genomic annotated files (VCF). Once you annotated your files using SnpEff, you can use SnpSift to help you filter large genomic datasets in order to find the most significant variants
Required Modules
Serial
- snpeff
System Variables
- HPC_{{#uppercase:snpeff}}_DIR - main installation directory
- HPC_{{#uppercase:snpeff}}_BIN - directory with executable scripts
- HPC_{{#uppercase:snpeff}}_CONF - directory with the default configuration file.
Additional Information
For snpeff/3.3h we provided a 'snpeff' wrapper that made running snpeff easier. For example,
java -Xmx2g -jar $HPC_SNPEFF_DIR/jar/snpEff.jar download -c $HPC_SNPEFF_CONF/snpEff.config -v athalianaTair10
could be run simply as
snpeff download -v athalianaTair10
To override the default 2g java memory setting use the following command on the command-line or in a job script:
export _JAVA_OPTIONS="-Xmx4g"
In SnpEff-4.x series the upstream project provides a shell script 'snpEff', which can be used to run the program without calling java directly.
Citation
If you publish research that uses snpeff you have to cite it as follows:
SnpEff:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
SnpSift:
"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
Reference Databases
List of installed SnpEff databases for the current default snpEff version, which is loaded with 'module load snpeff'.
| Genome |
|---|
| 3.0.29 |
| Escherichia_coli_LF82_uid161965 |
| Escherichia_coli_LY180_uid219461 |
| Escherichia_coli_NA114_uid162139 |
| Escherichia_coli_O103_H2_12009_uid41013 |
| Escherichia_coli_O104_H4_2009EL_2050_uid175905 |
| Escherichia_coli_O104_H4_2009EL_2071_uid176128 |
| Escherichia_coli_O104_H4_2011C_3493_uid176127 |
| Escherichia_coli_O111_H__11128_uid41023 |
| Escherichia_coli_O127_H6_E2348_69_uid59343 |
| Escherichia_coli_O157_H7_EC4115_uid59091 |
| Escherichia_coli_O157_H7_EDL933_uid57831 |
| Escherichia_coli_O157_H7_TW14359_uid59235 |
| Escherichia_coli_O157_H7_uid57781 |
| Escherichia_coli_O26_H11_11368_uid41021 |
| Escherichia_coli_O55_H7_CB9615_uid46655 |
| Escherichia_coli_O55_H7_RM12579_uid162153 |
| Escherichia_coli_O7_K1_CE10_uid162115 |
| Escherichia_coli_O83_H1_NRG_857C_uid161987 |
| Escherichia_coli_P12b_uid162061 |
| Escherichia_coli_PMV_1_uid219679 |
| Escherichia_coli_S88_uid62979 |
| Escherichia_coli_SE11_uid59425 |
| Escherichia_coli_SE15_uid161939 |
| Escherichia_coli_SMS_3_5_uid58919 |
| Escherichia_coli_UM146_uid162043 |
| Escherichia_coli_UMN026_uid62981 |
| Escherichia_coli_UMNK88_uid161991 |
| Escherichia_coli_UTI89_uid58541 |
| Escherichia_coli_W_uid162011 |
| Escherichia_coli_W_uid162101 |
| Escherichia_coli_Xuzhou21_uid163995 |
| Escherichia_fergusonii_ATCC_35469_uid59375 |
| Ethanoligenens_harbinense_YUAN_3_uid46255 |
| Eubacterium_cylindroides_T2_87_uid197177 |
| Eubacterium_eligens_ATCC_27750_uid59171 |
| Eubacterium_limosum_KIST612_uid59777 |
| Eubacterium_rectale_ATCC_33656_uid59169 |
| Eubacterium_rectale_uid197161 |
| Eubacterium_rectale_uid197162 |
| Eubacterium_siraeum_uid197160 |
| Eubacterium_siraeum_V10Sc8a_uid197178 |
| Exiguobacterium_antarcticum_B7_uid176125 |
| Exiguobacterium_AT1b_uid59093 |
| Exiguobacterium_MH3_uid227425 |
| Exiguobacterium_sibiricum_255_15_uid58053 |
| Faecalibacterium_prausnitzii_L2_6_uid197183 |
| Faecalibacterium_prausnitzii_uid197157 |
| Ferrimonas_balearica_DSM_9799_uid53371 |
| Ferroglobus_placidus_DSM_10642_uid40863 |
| Ferroplasma_acidarmanus_fer1_uid54095 |
| Fervidicoccus_fontis_Kam940_uid162201 |
| Fervidobacterium_nodosum_Rt17_B1_uid58625 |
| Fervidobacterium_pennivorans_DSM_9078_uid78143 |
| Fibrella_aestuarina_uid178352 |
| Fibrobacter_succinogenes_S85_uid161919 |
| Fibrobacter_succinogenes_S85_uid41169 |
| Filifactor_alocis_ATCC_35896_uid46625 |
| Finegoldia_magna_ATCC_29328_uid58867 |
| Flavobacteriaceae_bacterium_3519_10_uid59413 |
| Flavobacteriales_bacterium_HTCC2170_uid51877 |
| Flavobacterium_branchiophilum_FL_15_uid73421 |
| Flavobacterium_columnare_ATCC_49512_uid80731 |
| Flavobacterium_indicum_GPTSA100_9_uid157999 |
| Flavobacterium_johnsoniae_UW101_uid58493 |
| Flavobacterium_psychrophilum_JIP02_86_uid61627 |
| Flexibacter_litoralis_DSM_6794_uid168257 |
| Flexistipes_sinusarabici_DSM_4947_uid68147 |
| Fluviicola_taffensis_DSM_16823_uid65271 |
| Francisella_cf__novicida_3523_uid162107 |
| Francisella_cf__novicida_Fx1_uid162105 |
| Francisella_noatunensis_orientalis_LADL_07_285A_uid231515 |
| Francisella_noatunensis_orientalis_Toba_04_uid164779 |
| Francisella_novicida_U112_uid58499 |
| Francisella_philomiragia_ATCC_25017_uid59105 |
| Francisella_tularensis_FSC198_uid58693 |
| Francisella_tularensis_holarctica_F92_uid181998 |
| Francisella_tularensis_holarctica_FSC200_uid54341 |
| Francisella_tularensis_holarctica_FTNF002_00_uid58999 |
| Francisella_tularensis_holarctica_LVS_uid58595 |
| Francisella_tularensis_holarctica_OSU18_uid58687 |
| Francisella_tularensis_mediasiatica_FSC147_uid58939 |
| Francisella_tularensis_NE061598_uid161973 |
| Francisella_tularensis_SCHU_S4_uid57589 |
| Francisella_tularensis_TI0902_uid89373 |
| Francisella_tularensis_TIGB03_uid89379 |
| Francisella_tularensis_WY96_3418_uid58811 |
| Francisella_TX077308_uid68321 |
| Frankia_alni_ACN14a_uid58695 |
| Frankia_EAN1pec_uid58367 |
| Frankia_EuI1c_uid42615 |
| Frankia_symbiont_of_Datisca_glomerata_uid46257 |
| Frateuria_aurantia_DSM_6220_uid81775 |
| GCA_000006665.1.29 |
| GCA_000008865.1.29 |
| GCA_000010825.1.29 |
| GCA_000010845.1.29 |
| GCA_000010865.1.29 |
| GCA_000010885.1.29 |
| GCA_000010905.1.29 |
| GCA_000010925.1.29 |
| GCA_000010945.1.29 |
| GCA_000010965.1.29 |
| GCA_000015025.1.29 |
| GCA_000015325.1.29 |
| GCA_000016725.1.29 |
| GCA_000018105.1.29 |
| GCA_000018785.1.29 |
| GCA_000020825.1.29 |
| GCA_000021125.1.29 |
| GCA_000021485.1.29 |
| GCA_000022225.1.29 |
| GCA_000022305.1.29 |
| GCA_000022565.1.29 |
| GCA_000023265.1.29 |
| GCA_000024985.1.29 |
| GCA_000025305.1.29 |
| GCA_000067165.1.29 |
| GCA_000091125.1.29 |
| GCA_000143765.1.29 |
| GCA_000144695.1.29 |
| GCA_000144915.1.29 |
| GCA_000147835.3.29 |
| GCA_000155125.1.29 |
| GCA_000159515.1.29 |
| GCA_000164035.1.29 |
| GCA_000165835.1.29 |
| GCA_000171915.1.29 |
| GCA_000171935.1.29 |
| GCA_000171955.1.29 |
| GCA_000171975.1.29 |
| GCA_000171995.1.29 |
| GCA_000172015.1.29 |
| GCA_000172035.1.29 |
| GCA_000172055.1.29 |
| GCA_000174215.1.29 |
| GCA_000175235.1.29 |
| GCA_000175575.2.29 |
| GCA_000176855.2.29 |
| GCA_000179815.2.29 |
| GCA_000181735.1.29 |
| GCA_000181755.1.29 |
| GCA_000181775.1.29 |
| GCA_000182805.2.29 |
| GCA_000186185.1.29 |
| GCA_000186945.1.29 |
| GCA_000187285.4.29 |
| GCA_000187305.2.29 |
| GCA_000187325.2.29 |
| GCA_000187385.2.29 |
| GCA_000188075.1.29 |
| GCA_000188115.2.29 |
| GCA_000190435.1.29 |
| GCA_000192845.1.29 |
| GCA_000193245.2.29 |
| GCA_000202835.1.29 |
| GCA_000208385.1.29 |
| GCA_000213215.1.29 |
| GCA_000214095.3.29 |
| GCA_000219125.2.29 |
| GCA_000219295.2.29 |
| GCA_000219745.1.29 |
| GCA_000221025.1.29 |
| GCA_000223485.1.29 |
| GCA_000225485.1.29 |
| GCA_000230275.1.29 |
| GCA_000236685.1.29 |
| GCA_000236785.2.29 |
| GCA_000241585.2.29 |
| GCA_000241625.2.29 |
| GCA_000242635.3.29 |
| GCA_000245075.1.29 |
| GCA_000247605.1.29 |
| GCA_000264945.1.29 |
| GCA_000271325.1.29 |
| GCA_000281715.1.29 |
| GCA_000286415.1.29 |
| GCA_000306035.1.29 |
| GCA_000313135.1.29 |
| GCA_000320565.2.29 |
| GCA_000382885.1.29 |
| GCA_000411395.1.29 |
| GCA_000416985.1.29 |
| GCA_000418325.1.29 |
| GCA_000421925.1.29 |
| GCA_000445065.1.29 |
| GCA_000445085.1.29 |
| GCA_000445105.1.29 |
| GCA_000445145.1.29 |
| GCA_000468835.1.29 |
| GCA_000508185.1.29 |
| GCA_000508285.1.29 |
| GCA_000517425.1.29 |
| GCA_000588875.1.29 |
| GCA_000614805.1.29 |
| GCA_000616745.1.29 |
| GCA_000617205.1.29 |
| GCA_000617585.1.29 |
| GCA_000617865.1.29 |
| GCA_000617965.1.29 |
| GCA_000617985.1.29 |
| GCA_000618025.1.29 |
| GCA_000618045.1.29 |
| GCA_000618065.1.29 |
| GCA_000618105.1.29 |
| GCA_000618145.1.29 |
| GCA_000618185.1.29 |
| GCA_000618205.1.29 |
| GCA_000618225.1.29 |
| GCA_000618245.1.29 |
| GCA_000618265.1.29 |
| GCA_000618285.1.29 |
| GCA_000618305.1.29 |
| GCA_000618325.1.29 |
| GCA_000618345.1.29 |
| GCA_000618365.1.29 |
| GCA_000618385.1.29 |
| GCA_000618425.1.29 |
| GCA_000618445.1.29 |
| GCA_000618465.1.29 |
| GCA_000618485.1.29 |
| GCA_000618505.1.29 |
| GCA_000618525.1.29 |
| GCA_000618545.1.29 |
| GCA_000618565.1.29 |
| GCA_000618585.1.29 |
| GCA_000618605.1.29 |
| GCA_000618625.1.29 |
| GCA_000618645.1.29 |
| GCA_000618665.1.29 |
| GCA_000618685.1.29 |
| GCA_000618745.1.29 |
| GCA_000618765.1.29 |
| GCA_000618785.1.29 |
| GCA_000618805.1.29 |
| GCA_000618825.1.29 |
| GCA_000618845.1.29 |
| GCA_000618865.1.29 |
| GCA_000618885.1.29 |
| GCA_000618925.1.29 |
| GCA_000619365.1.29 |
| GCA_000619385.1.29 |
| GCA_000619405.1.29 |
| GCA_000619425.1.29 |
| GCA_000619445.1.29 |
| GCA_000619685.1.29 |
| GCA_000632125.2.29 |
| GCA_000632555.1.29 |
| GCA_000632655.1.29 |
| GCA_000633575.2.29 |
| GCA_000689195.1.29 |
| GCA_000691125.1.29 |
| GCA_000722875.1.29 |
| GCA_000723785.1.29 |
| GCA_000724705.1.29 |
| GCA_000730345.1.29 |
| GCA_000732965.1.29 |
| GCA_000743655.1.29 |
| GCA_000743885.1.29 |
| GCA_000747525.1.29 |
| GCA_000755665.1.29 |
| GCA_000755675.1.29 |
| GCA_000757485.1.29 |
| GCA_000757725.1.29 |
| GCA_000758265.1.29 |
| GCA_000783435.1.29 |
| GCA_000787395.1.29 |
| GCA_000803705.1.29 |
| GCA_000827215.1.29 |
| GCA_000938735.1.29 |
| GCA_000945115.1.29 |
| GCA_000949015.1.29 |
| GCA_000949295.1.29 |
| GCA_000953195.1.29 |
| GCA_000963905.1.29 |
| GCA_000964345.1.29 |
| GCA_000964385.1.29 |
| GCA_000967095.1.29 |
| GCA_000967915.1.29 |
| GCA_000968055.1.29 |
| GCA_001005725.1.29 |
| GCA_001005835.1.29 |
| GCA_001006065.1.29 |
| GCA_001038045.1.29 |
| GRCh38.82 |
| GRCh38.p2.RefSeq |
| hg19 |
| SL2.50 |
| Sorbi1.29 |
| todo_db.txt |
| todo_db.txt.orig |
| Vibrio_EJY3_uid83161 |