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Call and score variants from WGS/WES of rare disease patients.
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
Dockstore implementation of CGP core WGS analysis
Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)
acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.
Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)
Extract and explore snv data
Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).
Estimates the clonal population structure in a tumour sample given a cell mutation matrix
Genome assembly and variant benchmarks for Chinese Quartet
Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in pure Python.
An adaptable method for analyzing SNVs, INDELs, and CNVs from Whole Exome Sequencing (WES) data, emphasizing germline variants.
In this repository I backup the pipelines I write for the project I am involved
Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.
a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow
maftools for SNV mutation analysis, summarizes, and visualization
This guide outlines a step-by-step process for managing your WordPress plugin to add/update in the WordPress repository using SVN (Subversion). SVN is a version control system that helps you track changes, collaborate with others, and maintain a history of your project.
Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md
GATK WGS workflow
Convert output from Samtools pileup into a matrix.
Diretório com os algoritmos de pré-processamento e modelos para análise de dados espectrais da uva de mesa Cotton Candy.
WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication
Predicting true low-VAF SNVs in HPV using triplicate NGS samples and machine learning
vue app with flask REST api to process genomic data
analysis of data on neutral single nucleotide polymorphisms