GavinHaLab

ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Griffin

A flexible framework for nucleosome profiling of cell-free DNA

ichorCNA_offtarget

Estimating tumor fraction by exploiting the off-target reads from targeted DNA sequencing.

SV_10X_analysis

Structural variation analysis of 10X Genomics linked-read data

SV_WGS_analysis

Structural variation analysis pipeline for cancer genomes

TitanCNA_10X_snakemake

Snakemake workflow for 10X Genomics WGS analysis using TitanCNA

ichorCNA_SV_WGS_tumorOnly

crpc-sv-pattern-study

CRPCSubtypingPaper

Analysis code used in ctDNA CRPC phenotype manuscript

pdx_evolution_study

This repository contains the scripts and data needed to reproduce the findings of our PDX evolution study.

PDX_mouseSubtraction

fastq_to_bam_paired_snakemake

A snakemake to convert paired fastq files to analysis-ready bams, following GATK best practices.

GavinHaLab.github.io

Gavin Ha Lab Website

Keraon

A tool for estimating heterogenous phenotype fractions from ctDNA features

mutect2_snakemake

A snakemake to run Mutect2 on analysis-ready bams, following GATK best practices.

SCLCpheno-seq_paper

TitanCNA_SV_WGS

WDL-Pipelines

A central repository for tools wrapped in WDL for the Ha lab.

Admixtures_snakemake

CDK12-CRPC-paper

downsampling_snakemake

fastq_to_bam_interleaved_snakemake

A snakemake to convert interleaved fastq files to analysis-ready bams, following GATK best practices.

gridss2_somatic_sv_call

ichorCNA_WDL

Has Dockerfile and WDL pipeline for ichorCNA

Sequencing_analysis_assignment

Sequencing analysis questions

TitanCNA_SV_WGS_tumorOnly

TritonNP

A tool for extracting region-based phasing features from cell-free DNA