Tag: snpsift

Obtain heterozygous variant frequencies from dbNSFP using snpsift 0 Dear colleague, I am using the dbNSFP (v4.2a) database to annotate the variants identified in WGS (homo sapiens) using snpsift. Unless I am mistaken, I cannot find the parameters to get heterozygous variant frequencies of gnomad from dbNSFP (v4.2a). I only…

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…

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…

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…

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…

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…

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,…

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 |…

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…