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whole_setup.md

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Raw

Data Preparation

  • This is data prepartion process for whole wokrflow. It is computationally intensive, so we would subset the data for demonstation purpose. The following codes is for those who want to practice whole, real-life WGS workflow
  • TL;DR : run following code
curl -o run.sh https://raw.githubusercontent.com/JiehoonKwak/MSE801_JHLEE/main/download.sh && chmod +x download.sh && ./download.sh

Raw sequence reads & reference genome download

  1. Download sequence reads using SRA explorer
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/000/SRR7138440/SRR7138440_1.fastq.gz -o SRR7138440_WES_of_homo_sapiens_blood_of_brain_tumor_patient_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/000/SRR7138440/SRR7138440_2.fastq.gz -o SRR7138440_WES_of_homo_sapiens_blood_of_brain_tumor_patient_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/008/SRR7138438/SRR7138438_1.fastq.gz -o SRR7138438_WES_of_homo_sapiens_subventricular_zone_of_brain_tumor_patient_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/008/SRR7138438/SRR7138438_2.fastq.gz -o SRR7138438_WES_of_homo_sapiens_subventricular_zone_of_brain_tumor_patient_2.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/005/SRR7138435/SRR7138435_1.fastq.gz -o SRR7138435_WES_of_homo_sapiens_tumor_of_brain_tumor_patient_1.fastq.gz
curl -L ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR713/005/SRR7138435/SRR7138435_2.fastq.gz -o SRR7138435_WES_of_homo_sapiens_tumor_of_brain_tumor_patient_2.fastq.gz
  1. Download reference genome
curl -L https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz -o hg38.fa.gz
  1. Download Base Quality Score Recalibration (BQSR)
curl -L https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf -o Homo_sapiens_assembly38.dbsnp138.vcf
curl -L https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx -o Homo_sapiens_assembly38.dbsnp138.vcf.idx
  1. Download Mutect2 resources
  • gnomeAD
curl -L https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/somatic-hg38/af-only-gnomad.hg38.vcf.gz -o af-only-gnomad.hg38.vcf.gz
curl -L https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi -o af-only-gnomad.hg38.vcf.gz.tbi
  • PoN
curl -L https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz -o 1000g_pon.hg38.vcf.gz
curl -L https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz.tbi -o 1000g_pon.hg38.vcf.gz.tbi
  • Interval files
curl -L https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.1.interval_list -o exome_calling_regions.v1.1.interval_list
  • Funcotator source file
gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download --hg38