snpEff on Biowulf
snpSift. SnpSift is a collection of tools to manipulate VCF (variant call format) files. Here's what you can do: ... Interactive jobs should be ...
snpEff on the NIH Biowulf cluster - GitHub Gist
snpEff on the NIH Biowulf cluster. GitHub Gist: instantly share code, notes, and snippets.
Scientific Applications on NIH HPC Systems
A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. ... snpEff is a variant ...
... snpeff \ --outdir /data/$USER/sarek/ \ --genome GATK.GRCh38 \ --igenomes_base /fdb/igenomes_nf \ --save_output_as_bam \ -w /lscratch/$SLURM_JOB_ID ...
Biowulf High Performance Computing at the NIH. GitHub · YouTube ... snpeff : Found 6 reports [INFO ] varianteval : Found 6 VariantEval ...
SnpEff & SnpSift - GitHub Pages
SnpEff. Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins ( ...
Working with VCF files - seqTools's documentation!
snpEff¶. Download data¶. java -jar /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.jar download -c /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.config ...
snippy: rapid haploid variant calling and core genome alignment
... snpEff - /opt/conda/envs/snippy/bin/ ... [user@cn3200 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$. Last modified: 12 ...
Biostars Software Reference - Bioinformatics for Beginners 2022
To complement this course, we have created a Biostars module on Biowulf. The ... snpEff · sra-tools · STAR · subread · trimmomatic · ucsc-bedgraphtobigwig · wget.
NCI-CGR/PLP_prediction_workflow - GitHub
Biowulf modules · bcftools/1.13 · annovar/2020-06-08 · snpEff/5.1d · csvkit/1.0.7 ...
samtools is used for working with SAM, BAM, and CRAM files containing aligned sequences. It can also be used to index fasta files. bcftools is ...
Plink is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes.
MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p- ...
Pascal (Pathway scoring algorithm) is an easy-to-use tool for gene scoring and pathway analysis from GWAS results. Pascal uses external data ...
2.2.1 snpEff. Download data java -jar /data/CCRBioinfo/biowulf/local/snpEff_3_0/snpEff.jar download -c /data/CCRBioinfo/biowulf/local/snp. Run ...
RFMIX is a program to identify the ancestry of genomic segments using random forest discriminative machine learning methods combined with a conditional random ...
VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and ...
biowulf Configuration. nf-core pipelines such as sarek have been successfully tested on the Biowulf cluster at the NIH.
A genome-first approach to characterize DICER1 pathogenic variant ...
DICER1 variant annotation, classification, and control selection. All DICER1 variants were annotated using snpEFF and ANNOVAR. Gene annotation was based on ...