In this repository I backup the pipelines I write for the project I am involved
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Updated
May 24, 2024 - Python
In this repository I backup the pipelines I write for the project I am involved
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Evaluating Nanopore-based bacterial variant calling
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Python library to facilitate genome assembly, annotation, and comparative genomics
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
bcftools for dealing with bcf files.
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
Convert genomic coordinates from the Human Genome version 19 (hg19) to version 38 (hg38)
Clair3-RNA - a long-read small variant caller for RNA sequencing data
A WDL-based workflow for extraction of variants and their associated info from large VCF files
Clair3-Trio: variant calling in trio using Nanopore long-reads
Create png file of variants proportions in an assembly/reference including CDS positions using output of vadr 1.5.1 (annotation) and vardict-java 1.8.3 (variant calling)
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
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