vcfeval_hap.py

hap.py version

v0.3.9 (Docker: https://hub.docker.com/r/pkrusche/hap.py/)

What does this app do?

Compares a query VCF to a truth VCF to calculate performance metrics including sensitivity and precision using hap.py and vcfeval. It is equivalent to running the precisionFDA GA4GH benchmarking app in 'vcfeval-partialcredit' mode with other options left as default. More information available at the following links:

• https://precision.fda.gov/apps/app-F5YXbp80PBYFP059656gYxXQ
• https://github.com/ga4gh/benchmarking-tools/tree/master/doc/ref-impl

What are typical use cases for this app?

Validating an NGS workflow using the NA12878 (NIST Genome in a Bottle) benchmarking sample.

What data are required for this app to run?

Input files:

1. A query VCF (.vcf | .vcf.gz) - output from the workflow being validated
2. A truth VCF (.vcf | .vcf.gz)
3. A panel BED file (.bed) - region covered in query vcf
4. A high confidence region BED file (.bed) - high confidence region for truth set

Parameters:

1. Skip - default = false. If set to true will exit without performing any analysis
2. Output files prefix (required)
3. Output folder (optional)
4. Indication if additional stratification for NA12878 samples should be performed (default = False)
   • If truth set is NA12878, additional stratification of results can be performed and output in extended.csv file
   • HOWEVER the instance type will need to be upgraded to have at least 7GB of RAM, and the app will take significantly longer to run
5. Reference Genome build GRCh37 (default) or GRCh38

Note:

• The BED file names must not contain spaces or characters such as + and -

What does this app output?

This app outputs:

1. Summary csv file containing separate performance metrics for SNPs and Indels
2. Summary report HTML (generated using ga4gh rep.py https://github.com/ga4gh/benchmarking-tools/tree/master/reporting/basic)
3. Detailed results folder containing:
   • Extended csv file - Including results stratification and confidence intervals
   • VCF file - annotated vcf showing TP, FP and FN variants
   • runinfo JSON - detailed information about hap.py run
   • version log - version numbers of software used in app
   • metrics JSON - JSON file containing all computed metrics and tables

How does this app work?

• 'chr' is stripped from the chromosome field of the VCF and BED files (if hg19 format used)
• Indexed and zipped VCF files passed to hap.py:
  • Uses vcfeval comparison engine
  • If the sample is NA12878, additional stratification is performed using bed files found here: https://github.com/ga4gh/benchmarking-tools/tree/master/resources/stratification-bed-files
  • Summary HTML is generated

What are the limitations of this app

• Only works with inputs mapped to GRCh37 or GRCh38

This app was made by Viapath Genome Informatics