Discover ding-lab/BreakPointSurveyor Open Source project

Characterization of Germline variants

121

CharGer

identifying mutational significance in cancer genomes

MuSiC2

3D hotspot mutation proximity analysis tool

hotspot3d

Detect somatic variants from tumor and normal WGS/WXS data

PanCanAtlasGermline

GenomeVIP

PHP

somaticwrapper

BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

PanCan_snATAC_publication

Jupyter Notebook

BICSEQ2

Variant quality checking scripts.

VariantQC

call copy number from WES(WXS)

cnvkit_pipeline

Discover Mutation Induced Splice Sites

misplice

predict neoantigen for indel and snvs

neoscan

VirusScan

VirusScan Pipeline

Methylation array analysis pipeline for CPTAC

cptac_methylation

TinDaisy

CWL somatic variant caller

Common Workflow Language

gatk4wxscnv

Pipeline for WXS CNV using GATK4

germline_variant_snakemake

Snakemake workflow to call germline variant

Improved Bayesian inversion somatic caller

ccRCC_snRNA_analysis

bassovac

Detection of chimeric transcripts (aka fusions) from barcoded single cell RNA-seq

fuscia

Suite of fusion gene analysis tools

griffin-fusion

CPTAC3-RNA-related-pipeline

Gene/transcript expression; Fusion; de novo assembly

Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA

mc3_icgc_variant_pipeline

germlinewrapper

detect germline variants from normal samples

Cohort DNA Copy Number Analysis

cmds

birdseed2vcf

Convert birdseed variant file with genotypes to a VCF file

CWL germline variant caller

TinJasmine

Common Workflow Language

MIRMMR

Microsatellite Instability Regression using Methylation and Mutations in R

HotPho_Analysis

HotPho, a bioinformatics tool to discover spatially interacting phosphorylation sites and mutations in cancer

SomaticSV

CWL wrapper for Manta 1.4.0 and simple filter

miRNA sequencing analysis for CPTAC

CPTAC_miRNA

Automatic FASTQ to BAM pipeline (regular WES/WGS, 10x WES/WGS)

FASTQtoBAM

Script to format KEGG pathway data for PathScan

parse-kegg

Detecting break points of large deletions and medium sized insertions from paired-end short read

pindel2

Modify fields of Varscan VCF files. CWL implementation

varscan_vcf_remap

A tool that classifies cells based on their gene expression

pollock

infer_cnv_postprocesssing

Ancestry prediction from .bam files

ancestry

Jupyter Notebook

10Xmapping

mapping somatic variants to cell barcodes in scRNA-Seq data

Automated download of CPTAC3 data from GDC

importGDC

Given two BAM files, a reference sequence, and regions of interest, count the AT, CG, or CpG sites with sufficient read-depth in both BAMs.

calc-roi-covg

gdc_qc_analysis

Somatic mutation pipeline comparison of TCGA samples between Genomic Data Commons (GDC) and MC3

RMarkdown

hotspot3d_portal

JavaScript

VEP_Filter

TinDaisy modules for filtering VCF based on VEP annotation

Identifying significantly deleterious variants from germline variation and somatic mutational events

PDX-PanCanAtlas

Jupyter Notebook

rareprob2

TinDaisy-Core

Core somatic caller scripts based on SomaticWrapper CWL branch

Fusion_hg38

Convert Pindel data into SAM & BAM formats.

SalmonTE

Pindel2BAM

Directory hosting scripts used for phosphoproteomics analysis.

phosphoproteomics

PDXToolkit

CPTAC RNA expression pipeline

cptac_rna_expression

druggability_databases

CWL tool for calling germline variants using GATK

GATK_GermlineCaller

CWL wrapper for VEP annotation

VEP_annotate

Common Workflow Language

LR-PKD

Analysis pipeline for haplotype-based variant detection

Obtain submitted reads and clinical info associated with CPTAC3 cases

GDC.case.discover

SV Detection for soft-clipped genomic or cDNA reads

phospho-signaling

squaredancer

Comprehensive QC of CPTAC3 sequence data

CPTAC3_QC

Detect Virus integration site

VirusIntegrate

Scripts for managing Cromwell workflows

CromwellRunner