cnvkit

Here are 6 public repositories matching this topic...

XUKEREN / phd-pipeline

Some workflows I wrote for my phd projects

bioinformatics gatk variant-calling copy-number-variation eqtl structural-variation mutational-signatures mqtl ewas epigentics cnvkit

Updated Jul 30, 2023
Shell

pedricolino / cnakepit

Star

A Snakemake pipeline for copy number variant calling without normal tissue samples

bioinformatics snakemake conda cnv bwa panels cna mutect2 targeted-sequencing sequencing-data cnvkit copynumbervariation purecn

Updated Jul 31, 2025
Python

homijan / apm-cnv

Star

CNV callers for cfDNA

r canary python3 ichorcna cnvkit wisecondor

Updated May 14, 2022
Python

shengqin / my_AI_agent

Star

cfDNA somatic variant calling (Mutect2 + PoN, CNVkit, Manta, CAPP-Seq filtering, CHIP flagging, tumor fraction) and tumor-microbiome RNA-seq pipelines (Kraken2/Bracken + Kaiju) on SLURM/HPC

bioinformatics hpc slurm metagenomics gatk ctdna cfdna mutect2 liquid-biopsy kraken2 lymphoma cnvkit somatic-variant-calling

Updated Oct 15, 2026
Shell

aliciapalominomosquera / apm-cnv

Star

CNV callers for cfDNA

r canary python3 ichorcna cnvkit wisecondor

Updated Nov 10, 2022
Python

twanapip / NGS-seq-tutorial

Star

Beginner-friendly WGS/WES tutorial: raw reads to filtered, annotated variants with BWA + GATK. Also somatic (Mutect2), CNV, GWAS. Workstation and Slurm scripts.

Updated Oct 28, 2026
Shell

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