Small GATK alignment and variant calling pipeline using python
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Updated
Jul 18, 2022 - Python
Small GATK alignment and variant calling pipeline using python
Perform read mapping and variant calling using snippy
Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"
NextFlow pipeline for mitochondria sequence reconstruction
Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.
command line and desktop tool for microbial variant calling
Efficiently detecting genomic structural variants (SVs) is a key step to grasp the "missing heritability" underlying complex traits involved in major evolutionary processes such as speciation, phenotypic plasticity, and adaptive responses. We present a random forest ensemble method for accurate deletion identification. We called this approach RF…
A toolset for data pipelines in Genomics
Variant calling of WGS datasets
Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5
A chamada de variantes envolve a identificação de polimorfismos de nucleotídeo único (SNPs) e pequenas inserções e deleções (indels) em dados de Sequenciamento de Nova Geração (NGS). Nesta pipeline descrevo a detecção de SNP para identificação de possíveis alterações de aminoácidos em proteínas virais.
Multi-class classification of drug resistance in MTB clinical isolates
Clair3-RNA - a long-read small variant caller for RNA sequencing data
A collection of data sets for benchmarking de novo variant discovery tools
Script to convert Duplex Sequencing .mutpos file formats into valid VCF files
A python script for generating sample VCF data based on a template VCF
Obtaining case-associated variants and correspondent genes (from control/case experiments) in BASH/R enviroment
Filter a VCF to discard false positive variants
Snake Genotyping By Sequencing. A reimplementation of Fast-GBS using snakemake.
A simple tool for SNP mutation type determination.
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