Activity for snpEff
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dan modified a comment on discussion General Discussion
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...
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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...
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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...
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snpEff released /snpEff_v4_5covid19_core.zip
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Raheel Ahmad posted a comment on discussion General Discussion
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?
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Jean-Charles Isner posted a comment on discussion General Discussion
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...
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Sann posted a comment on discussion General Discussion
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
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David Yarmosh posted a comment on discussion General Discussion
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.<init>(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:680) at org.snpeff.snpEffect.Config.readConfig(Config.java:648)...
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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
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Sun posted a comment on discussion General Discussion
I am getting this error with gff database: $JAVA -jar snpEff.jar build -gff3 -v Corynespora...
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Annemarie Eckes posted a comment on discussion General Discussion
After doing $ java -jar snpEff.jar databases I found that there was a database available...
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