VCFscope

VCFscope is a tool to investigate and report on the performance of a genome analysis pipeline. It does this by comparing variant calls (in vcf format, with a matched BAM file) generated by an analytical pipeline, to variant calls from a gold standard. Currently this is limited to germline sequencing of NA12878, compared to the GiaB consortium gold-standard reference. This DNAnexus app produces a raw data file (R's RDS format) that is then processed by VCFScope Report to make a detailed human-readable report.

Inputs

• [Required] vcfgz: A .vcf.gz of variants called in an NA12878 sample. This must be a single-sample VCF file.
• [Required] bam: A .bam of mapped reads used to generate the variants above.
• [Required] bai: A .bai index for the BAM file above.
• [Optional] region: A .bed file of genomic intervals; only variants overlapping at least one of these intervals will be considered in calculations. If missing, the entire genome and reportable range are considered.

vcfscope_reporter_resources_bundle-2.0.tar

The app unpacks a tar bundle, which contains:

• the NIST v2.19 vcf and bed file

• mdust low complexity regions

• hs37d5 reference genome, in RTG format

• reportable range files, as defined by Garvan

• RTG executable

  ├── gold_standard │   ├── calls-2.19.vcf.gz │   ├── calls-2.19.vcf.gz.tbi │   └── valid_regions-2.19.bed.gz ├── redundant_regions │   └── mdust.bed.gz ├── reference │   └── hs37d5.sdf │   ├── done │   ├── format.log │   ├── mainIndex │   ├── namedata0 │   ├── nameIndex0 │   ├── namepointer0 │   ├── progress │   ├── seqdata0 │   ├── seqdata1 │   ├── seqdata2 │   ├── seqdata3 │   ├── seqpointer0 │   ├── seqpointer1 │   ├── seqpointer2 │   ├── seqpointer3 │   ├── sequenceIndex0 │   ├── suffixdata0 │   ├── suffixIndex0 │   ├── suffixpointer0 │   └── summary.txt ├── reportable_range │   ├── genome.bed.gz │   └── reportable_range.bed └── rtg-tools └── RTG.jar

R package dependencies

• This has been tested extensively with R 3.2.0, and more recently, but to less extent, R 3.2.3. The R package dependencies are captured within the vcfscope-asset/Makefile.

Output

• RDS of performance metrics.