Cancer Risk Predictor

Detailed Guide 详细说明

Workflow Overview 工作流概览

This tool triggers a comprehensive genomic analysis pipeline for cancer risk prediction. The workflow includes:

• Quality Control: FastQC for initial quality assessment
• Read Trimming: fastp 1.1.0 for adapter trimming and quality filtering
• Alignment: BWA-MEM2 v2.3 for mapping reads to reference genome
• Variant Calling: GATK 4.6.2.0 best practices pipeline
• Analysis: Variant annotation and risk prediction

Input Requirements 输入要求

FASTQ Files Format: Must be compressed with .fastq.gz extension ( .fq.gz is not supported ). Both single-end and paired-end reads are supported.

Directory Structure: All FASTQ files must be placed in a root folder named fastq. Each sample's files need to be stored in a separate subdirectory under fastq (required for parallel running).

File Naming Convention: Paired-end reads should be named R1.fastq.gz and R2.fastq.gz in the sample subdirectory. Example structure:

                        fastq/sample1/sample1.R1.fastq.gz
                        fastq/sample1/sample1.R2.fastq.gz
                        fastq/sample2/sample2.R1.fastq.gz
                        fastq/sample2/sample2.R2.fastq.gz
                        

Folder Permission: The root fastq folder must be set to permissions 757 or 777 to allow read and write access for the Docker container.

Reference Genome 参考基因组

The reference directory (/mnt/d1/pool/sun/ghrunner/lyx/ref/hg38/) must contain the following hg38 files for fastq-fastp-bwa-gatk pipeline, with index files paired (required for BWA and GATK running):

1. FASTA sequence + BWA/GATK indexes (core for genome alignment)
   hg38.fa, hg38.fa.amb, hg38.fa.ann, hg38.fa.pac, hg38.fa.fai
2. GATK required sequence dictionary
   hg38.dict (or Homo_sapiens_assembly38.dict, both are applicable)
3. Known variant databases (compressed VCF + tabix index .tbi) (for GATK base quality recalibration and variant filtering)
   • dbSNP database: dbSNP.hg38.vcf.gz + dbSNP.hg38.vcf.gz.tbi
   • 1000G gold standard indels: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz + Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi