Category: SnpEff

filter multiple VCF files using snpSift

filter multiple VCF files using snpSift 1 Hi, I have several hundreds annonated VCF files (annotated using snpEff). I want to filter out all the low quality and low impact variants in all VCF files. Is there a way to  filter all files at one time, rather than filtering each…

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Sanity check his should never happen

Issues generating the annotated.eff.vcf file : Sanity check his should never happen 0 Hello, I am having a hard time deciphering the error associated with the vcf annotation file. I used the command: java -Xmx8g -jar snpEff.jar Tair10.1 /globalhome/cae453/HPC/sample6.vcf > /globalhome/cae453/HPC/sample6.eff.vcf The output is java.lang.RuntimeException: Sanity check: This should never…

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S. cerevisiae in snpEff databases

S. cerevisiae in snpEff databases 0 On snpEff 5.0, if you do java -jar snpEff.jar databases and look for Saccharomyces cerevisiae, you will find (among many other entries): R64-1-1.75 Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_R64-1-1.75.zip R64-1-1.99 Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_R64-1-1.99.zip Saccharomyces_cerevisiae Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Saccharomyces_cerevisiae.zip The entry that is simply named Saccharomyces_cerevisiae — what is it? Is it…

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Extract variant consequence count from gnomad and patient VCF file

Hello, I have 2 types of VEP annotated VCF file – regular vcf and gnomad genome file. I would like to extract counts of both missense, synonymous, upstream and intron variants for each gene in each file. Output should be something similar to this: MHTFR: missense 23, intron 100, synonymous…

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Reference genome version between variant calling and annotation

Question: Reference genome version between variant calling and annotation 0 Dear colleagues, My project is focused on the annotation of human genetic variants (SNPs and short InDels) of WGS and WES. I am using SNPEff version 5.0. In the snpeff config file I found GCA_000001405.28_GRCh38.p13 Homo sapiens (hg38) (UCSC). In…

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Running SnpSift in parallel

Running SnpSift in parallel 0 Hi, I am trying to using SnpSift to calculate case vs control groups. The file I am using is quite large and the first time I ran SnpSift on the file took quite a few days to finish. I am in a bit of a…

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snpEff: annottation problem

snpEff: annottation problem 0 Hi everyone. I am using snpEff on my personal computer, and when I try to annotate a VCF file I get this error: [[0Kjava.lang.OutOfMemoryError: Java heap space[[0KM at java.util.Arrays.copyOfRange(Unknown Source)[[0KM at java.lang.String.<init>(Unknown Source)[[0KM at java.lang.StringBuilder.toString(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at org.snpeff.fileIterator.LineFileIterator.readNext(LineFileIterator.java:46)[[0KM [[0K at…

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snpEFF not able to download GRCH38 ?

snpEFF not able to download GRCH38 ? 2 HI Why snpEff not able to download GRCH38 ? Always its showing error, But its work well with GRCH37 reference. Thanks for your comments. likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ 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:681) at org.snpeff.snpEffect.Config.readConfig(Config.java:649) at…

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

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wont recognize the gtf or gff3 files (runtime exception)

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

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Case Control count per variant

Case Control count per variant 0 Hi, I was wonder if there was any software out there that will count the number of samples in a group that are homozygous ref, heterozygous, or homozygous for a variant an output result in a text file? In the past, I have been…

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phase_trio.sh | searchcode

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

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Variant filtration software

There are tools like ANNOVAR, SnpEff, and VEP that are widely used for variant annotation. Most variant filtration/prioritization software work on the output from these three main software. Appended below is a list of software that one can use to do variant annotation, filtration, and even prioritization. NOTE: However you…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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VCF Filter On Small Genomes

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…

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