NIAGADS
  • VCPA
  • Introduction
  • Step 1: Set up the Amazon Web Services (AWS) environment
    • 1.1 Create AWS account
    • 1.2 Configure your computing environment and login to AWS
    • 1.3 Setup a S3 bucket (simple storage solution for AWS) for hosting sequencing data
    • 1.4 Install AWS command line software for accessing S3 bucket via command line interface
    • 1.5 Install StarCluster for AWS instance provisioning (optional)
  • Step 2: Create your tracking database instance
    • Option 1: Setup sample tracking database using Public AMI (recommended)
    • Option 2: Setup sample tracking database using Docker
  • Step 3: Configure your project information in the tracking database
    • 3.1 List all projects in the tracking database
    • 3.2 Create the project in the tracking database
  • Step 4: Upload sequencing data to your S3 bucket
  • Step 5: Configure your samples information in the tracking database
    • 5.1 Input the sample information to the tracking database
    • 5.2 Populate the tracking database with the S3 paths for the samples to be processed
    • 5.3 Populate the tracking database with the designated result folder for each sample to be processed
    • 5.4 Input PCR protocol information into the tracking database
    • 5.5 Add the capture kit information (WES sample only) into the tracking database
    • 5.6 Generate an ID to represent the capture kit information (WES sample only)
  • Step 6: Submit a job to process one whole genome (WGS) / whole exome (WES) sample
    • 6.1 Update vcpa-pipeline bitbucket contents
    • 6.2 Choose which workflow to use
    • 6.3 Enter your AWS credentials into the workflow script
    • 6.4 Launch Amazon EC2 Spot Instances via starcluster
  • Step 7: Review quality metrics of processed data
  • Step 8: Generating Project-level VCF via joint genotyping
  • Optional: Change software versions and dependencies of the VCPA workflow
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  • Software
  • Dependency files

Optional: Change software versions and dependencies of the VCPA workflow

PreviousStep 8: Generating Project-level VCF via joint genotyping

Last updated 6 years ago

VCPA is functional equivalent to the CCDG/TOPMed protocol. VCPA is built upon the following default software versions and dependency files for variant call. We strongly recommend users to use these default versions.

Users can still change the default software versions using the JSON file if needed - see example shown at the bottom of the page.

Software

(version 0.7.15)

(version: 1.3.1-42-g0a15035(using htslib 1.3.2-135-g50db54b))

(version 3.7)

(version 2.8.1)

(version v0.6.5)

(version 0.1.12b)

(version 0.1.12b)

(version v1.0.13)

(version: 1.3.1-1)

Dependency files

Hg38 Reference genome version GRCh38DH

  • 1000 Genomes Project (3366 contigs)

  • md5sum: 64b32de2fc934679c16e83a2bc072064

GATK variant call hg38 dependency files

  • dbSNP annotation

  • Indels annotation

The example of JSON file: 

Tutorial_vcpa_steps.ref_alt : ## Path of the FASTA.alt alignment file
Tutorial_vcpa_steps.ref_amb : ## Path of the FASTA.amb alignment file
Tutorial_vcpa_steps.ref_ann : ## Path of the FASTA.ann alignment file
Tutorial_vcpa_steps.ref_bwt : ## Path of the FASTA.bwt alignment file
Tutorial_vcpa_steps.ref_pac : ## Path of the FASTA.pac alignment file
Tutorial_vcpa_steps.ref_sa :  ## Path of the FASTA.sa alignment file
Tutorial_vcpa_steps.ref_fai : ## Path of the FASTA.fai alignment file
Tutorial_vcpa_steps.ref_dict :  ## Path of the FASTA.dict alignment file
Tutorial_vcpa_steps.input_bam :  ## Path of the BAM/CRAM file 
Tutorial_vcpa_steps_steps.fastq_directory_path :  ## Path for the FASTQ file 
Tutorial_vcpa_steps.ref_fasta :  ## Path of the reference genome FASTA file 
Tutorial_vcpa_steps.TARGET : ## Path of the WES capture kit / target region file 
Tutorial_vcpa_steps.KNOWN : ## Path of the dbSNP 138 lifted Indel file 
Tutorial_vcpa_steps.KNOWN_index : ## Path of the dbSNP 138 lifted Indel index file
Tutorial_vcpa_steps.DBSNP : ## Path of the dbSNP 138 lifted SNV file
Tutorial_vcpa_steps.DBSNP_index :  ## Path of the dbSNP 138 lifted SNV index file
Tutorial_vcpa_steps.GOLD : ## Path of the Mills and 1000G gold standard indels file
Tutorial_vcpa_steps.GOLD_index : ## Path of the Mills and 1000G gold standard indels index file
Tutorial_vcpa_steps.BWA : ## Location of the BWA software
Tutorial_vcpa_steps.SAMBAMBA : ## Location of the SAMBAMBA software
Tutorial_vcpa_steps.SAMBLASTER : ## Location of the SAMBLASTER software
Tutorial_vcpa_steps.SAMTOOLS : ## Location of the SAMTOOLS software
Tutorial_vcpa_steps.PICARD : ## Location of the PICARD software
Tutorial_vcpa_steps.bamUtil : ## Location of the bamUtil software
Tutorial_vcpa_steps.GATK : ## Location of the GATK software
Tutorial_vcpa_steps.tmp : ## Location of the template
Tutorial_vcpa_steps.log : ## Location of the logs

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BWA
SAMTOOLS
GATK
PICARD
SAMBABA
SAMBLASTER
VCFTOOLS
BAMUTIL
BCFTOOLS
version
dbSNP 138 lifted SNV file
Corresponding index file
dbSNP 138 lifted Indel file
Corresponding index file
Mills and 1000G gold standard indels file
Corresponding index file