Activity for snpEff

dan modified a comment on discussion General Discussion

dan — Tue, 28 Jul 2020 01:49:14 -0000

Are we going to get the latest (patch 13) version of RefSeq GRCh38? If not, is there an easy way to build that reference myself for snpEff? I need consistency in my pipelines that are using RefSeq p13 hg38 UPDATE: I realized I was editing the wrong config file. This message will come up if the genome you're trying to build is not listed in the config file as per the snpEff docs Still would be nice to have a buit in refSeq GRCh38 patch 13 though in the default snpEff.config, the p7 FTP url points...

dan modified a comment on discussion General Discussion

dan — Tue, 28 Jul 2020 01:48:24 -0000

UPDATE: I realized I was editing the wrong config file. This message will come up if the genome you're trying to build is not listed in the config file as per the snpEff docs Are we going to get the latest (patch 13) version of RefSeq GRCh38? If not, is there an easy way to build that reference myself for snpEff? I need consistency in my pipelines that are using RefSeq p13 hg38 in the default snpEff.config, the p7 FTP url points here: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/ I believe this actually...

dan posted a comment on discussion General Discussion

dan — Mon, 27 Jul 2020 22:50:34 -0000

Are we going to get the latest (patch 13) version of RefSeq GRCh38? If not, is there an easy way to build that reference myself for snpEff? I need consistency in my pipelines that are using RefSeq p13 hg38 in the default snpEff.config, the p7 FTP url points here: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/ I believe this actually contains to the p13 patch of NCBI's data, indicated by the GCF accession IDs present in the FTP directory (haven't verified this) GCF_000001405.25_refseqgene_alignments.gff3...

snpEff released /snpEff_v4_5covid19_core.zip

snpEff — Thu, 16 Apr 2020 03:07:09 -0000

Raheel Ahmad posted a comment on discussion General Discussion

Raheel Ahmad — Tue, 21 Jan 2020 10:28:06 -0000

I downloaded the GRCh.92 database and unzipped it in my snpEff directory for the latest V4.3 release.. When using snpEff, I receive the error [0mjava.lang.RuntimeException: Property: 'GRCh38.92.genome' not found. However, it works with the manually downloaded GRCh38.86 file. Furthermore, GRCh38.92 is not listed in the available snpEff download tool list. Is there any way to use the 92 database at this time?

Jean-Charles Isner posted a comment on discussion General Discussion

Jean-Charles Isner — Mon, 04 Feb 2019 08:14:39 -0000

Hello, I have tried to annotate a genome but it seems that the stars (del) are not recognised by snpeff. Is this a bug? As an example, snpeff and snfsift gives this following table. Thanks, Charlie 198 Super-Scaffold_1 12465 . G ,A Broad_SNP_filter 1,0 1,0 9 7.77 A upstream_gene_variant MODIFIER g1547.t1 1 1095 -1 -1 -1 -1 199 Super-Scaffold_1 12465 . G ,A Broad_SNP_filter 1,0 1,0 9 7.77 A upstream_gene_variant MODIFIER g1545.t1 1 3924 -1 -1 -1 -1 200 Super-Scaffold_1 12465 . G ,A Broad_SNP_filter...

Sann posted a comment on discussion General Discussion

Sann — Tue, 24 Apr 2018 01:34:34 -0000

Hi, I am pretty new in this environment. I wonder if there is a Mycobacterium tuberculosis reference genome in snpeff database that can be used to annotate variants in .vcf format. I have downloaded recent version from here: http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

snpEff released /databases/v4_3/snpEff_v4_3_Hordeum_vulgare_v2.38.zip

snpEff — Tue, 27 Mar 2018 03:52:13 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Hordeum_vulgare.zip

snpEff — Tue, 27 Mar 2018 03:52:13 -0000

snpEff released /databases/v4_3/snpEff_v4_3_GRCh37.87.zip

snpEff — Mon, 19 Feb 2018 14:38:11 -0000

snpEff released /databases/v4_3/snpEff_v4_3_diachasma_alloeum.zip

snpEff — Tue, 30 Jan 2018 20:12:09 -0000

snpEff released /databases/v4_3/snpEff_v4_3_dioscorea_rotundata.zip

snpEff — Tue, 30 Jan 2018 18:02:09 -0000

snpEff released /snpEff_v4_3t_core.zip

snpEff — Fri, 24 Nov 2017 15:24:09 -0000

snpEff released /databases/v4_3/snpEff_v4_3_ITAG3.2.zip

snpEff — Tue, 07 Nov 2017 20:40:08 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Takifugu_rubripes.zip

snpEff — Wed, 01 Nov 2017 13:28:07 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Felis_catus.zip

snpEff — Tue, 24 Oct 2017 13:39:08 -0000

snpEff released /snpEff_v4_3s_core.zip

snpEff — Mon, 23 Oct 2017 16:09:06 -0000

snpEff released /snpEff_v4_3r_core.zip

snpEff — Wed, 06 Sep 2017 21:00:07 -0000

snpEff released /databases/v4_3/snpEff_v4_3_ASM185804v2.zip

snpEff — Mon, 04 Sep 2017 17:20:07 -0000

snpEff released /snpEff_v4_3q_core.zip

snpEff — Wed, 30 Aug 2017 14:16:07 -0000

David Yarmosh posted a comment on discussion General Discussion

David Yarmosh — Wed, 23 Aug 2017 19:41:22 -0000

I found plenty of H37Rv in the config file, but I'm not sure which value t use to download with the java -jar snpEff.jar download function. I also tried using the default example so i could get a feel for it, but something didn't work. $ java -jar snpEff.jar download GRCh38.76 java.lang.RuntimeException: Property: 'GRCh38.76.genome' not found at org.snpeff.interval.Genome.(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:680) at org.snpeff.snpEffect.Config.readConfig(Config.java:648)...

David Yarmosh posted a comment on discussion General Discussion

David Yarmosh — Wed, 23 Aug 2017 19:30:45 -0000

I was directed to SnpEff by this paper http://genomea.asm.org/content/4/4/e00657-16.full?sid=2d31c990-13c8-4941-8a5b-93f88acc8009#ref-6 which indicates they used SnpEff to annotate the H37Rv Mtb genome. I can't find this in the list of databases here on sourceforge. Am I not seeing it or is it labeled differently? The above paper does not indicate how they did so. Thanks, Dave

snpEff released /databases/v4_3/snpEff_v4_3_ahypochondriacus_v2.1.zip

snpEff — Fri, 11 Aug 2017 18:51:07 -0000

snpEff released /databases/v4_3/snpEff_v4_3_sscrofa11.1.zip

snpEff — Fri, 30 Jun 2017 19:37:35 -0000

snpEff released /databases/v4_3/snpEff_v4_3_GCF_000233375.1.zip

snpEff — Thu, 29 Jun 2017 14:31:43 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Propithecus_coquereli.zip

snpEff — Thu, 22 Jun 2017 14:02:07 -0000

snpEff released /snpEff_v4_3p_core.zip

snpEff — Tue, 06 Jun 2017 14:01:05 -0000

snpEff released /snpEff_v4_3o_core.zip

snpEff — Sun, 21 May 2017 13:51:07 -0000

snpEff released /snpEff_v4_3m_core.zip

snpEff — Fri, 05 May 2017 21:27:21 -0000

snpEff released /snpEff_v4_3l_core.zip

snpEff — Wed, 19 Apr 2017 16:18:08 -0000

snpEff released /snpEff_v4_3k_core.zip

snpEff — Wed, 29 Mar 2017 22:29:07 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Rhagoletis_zephyria.zip

snpEff — Fri, 17 Mar 2017 18:33:08 -0000

Sun posted a comment on discussion General Discussion

Sun — Fri, 03 Feb 2017 21:05:07 -0000

I am getting this error with gff database: $JAVA -jar snpEff.jar build -gff3 -v Corynespora...

snpEff released /snpEff_v4_3i_core.zip

snpEff — Fri, 16 Dec 2016 03:43:13 -0000

snpEff released /databases/v4_3/snpEff_v4_3_GRCh37.p13.RefSeq.zip

snpEff — Tue, 29 Nov 2016 03:11:10 -0000

snpEff released /snpEff_v4_3g_core.zip

snpEff — Mon, 28 Nov 2016 13:50:52 -0000

Annemarie Eckes posted a comment on discussion General Discussion

Annemarie Eckes — Mon, 28 Nov 2016 11:20:13 -0000

After doing $ java -jar snpEff.jar databases I found that there was a database available...

snpEff released /snpEff_v4_3f_core.zip

snpEff — Wed, 23 Nov 2016 21:41:10 -0000

snpEff released /snpEff_v4_3e_core.zip

snpEff — Sat, 19 Nov 2016 13:53:54 -0000

snpEff released /snpEff_v4_3c_core.zip

snpEff — Tue, 15 Nov 2016 16:14:12 -0000

snpEff released /databases/v4_3/snpEff_v4_3_ebola_zaire.zip

snpEff — Mon, 14 Nov 2016 19:40:09 -0000

snpEff released /databases/v4_3/snpEff_v4_3_KJ660346.1.zip

snpEff — Mon, 14 Nov 2016 19:40:09 -0000

snpEff released /databases/v4_3/snpEff_v4_3_WSB_EiJ_v1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:51 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Xipmac4.4.2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:51 -0000

snpEff released /databases/v4_3/snpEff_v4_3_turTru1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_TREESHREW.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_TETRAODON8.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_WBcel235.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_UMD2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_TENREC.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_vicPac1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_UMD3.1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:41 -0000

snpEff released /databases/v4_3/snpEff_v4_3_spetri2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_TENREC.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Sscrofa10.2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_SPRET_EiJ_v1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_taeGut3.2.4.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_tarSyr1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Rnor_6.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:33 -0000

snpEff released /databases/v4_3/snpEff_v4_3_proCap1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_PoeFor_5.1.2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_R64-1-1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_PPYG2.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_PWK_PhJ_v1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_pteVam1.86.zip

snpEff — Sun, 06 Nov 2016 12:16:25 -0000

snpEff released /databases/v4_3/snpEff_v4_3_OryCun2.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Orenil1.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_PapAnu2.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_PelSin_1.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_OtoGar3.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_Pmarinus_7.0.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_pika.86.zip

snpEff — Sun, 06 Nov 2016 12:16:17 -0000

snpEff released /databases/v4_3/snpEff_v4_3_LP_J_v1.86.zip