Category: snpsift

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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Missing some predictions based on dbNSFP v4.2a

Missing some predictions based on dbNSFP v4.2a 0 Hello everybody, I used dbNSFP v4.2a database for functional prediction and variant annotation. As mentioned in the download site sites.google.com/site/jpopgen/dbNSFP, this version compiles prediction scores from several prediction algorithms (SIFT, SIFT4G, Polyphen2-HDIV, Polyphen2-HVAR. ….), and other information, including allele frequencies observed in…

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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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adding allele frequencies to a vcf

adding allele frequencies to a vcf 1 Hi all, I have a vcf file generated from a few hundred samples. For each variant within the file, I would like to calculate the allele frequency of each allele and then add that information as a field into the ‘INFO’ field of…

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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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Annotate Structural variants with population specific allele frequency values

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

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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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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…

Continue Reading VCF Filter On Small Genomes

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…

Continue Reading VCF Filter On Small Genomes