VCF Comparison with Truvari Output¶

Pipeline Workflow¶

The flowchart illustrates the Truvari comparison pipeline for structural variant (SV) analysis. The Reference vs Modified VCF (that is output by the pipeline where reference and modified fasta are compared) serves as the baseline or truth-set, against which VCFs from PacBio, Nanopore, and Illumina sequencing are compared. The pipeline begins with sorting the VCF files (sort_vcf), indexing them (index_vcf), and then performing the Truvari comparison to generate the final comparison results.

Important! To allow the pipeline to run, set --run_truvari to true when launching the pipeline, or enable it in the data/valid/validated_params.json file:

By default, this parameter is set to false.

Directory Structure¶

truvari/
├── SampleName_sv_short_read.vcf.gz
├── SampleName_sv_short_read.vcf.gz.csi
├── SampleName.pacbio_sv_long_read.vcf.gz
├── SampleName.pacbio_sv_long_read.vcf.gz.csi
├── SampleName.ont_sv_long_read.vcf.gz
├── SampleName.ont_sv_long_read.vcf.gz.csi
├── ref_x_modsyri.vcf.gz
├── ref_x_modsyri.vcf.gz.csi
├── ref_x_modsyri_SampleName_sv_short_read_truvari       → folder comparing short-read SV pipeline with reference-to-modified fasta pipeline
├── ref_x_modsyri_SampleName.pacbio_sv_long_read_truvari → folder comparing PacBio long-read SV pipeline to reference-to-modified fasta pipeline
└── ref_x_modsyri_SampleName.ont_sv_long_read_truvari    → folder comparing Nanopore long-read SV pipeline to reference-to-modified fasta pipeline

Description¶

This folder contains all structural variant (SV) callsets and their Truvari benchmarking results comparing SVs detected from sequencing data with the structural variants derived from the reference vs modified genome comparison (SyRI).

Reference SV Callsets¶

ref_x_modsyri.vcf.gz¶

Structural variants derived from comparing the reference genome and the modified genome using SyRI.

SampleName_sv_short_read.vcf.gz¶

Structural variants detected from Illumina short reads.

SampleName.pacbio_sv_long_read.vcf.gz¶

Structural variants detected from PacBio long reads.

SampleName.ont_sv_long_read.vcf.gz¶

Structural variants detected from Oxford Nanopore long reads.

All .csi files represent index files for fast querying of VCF contents.

Truvari Comparison Result Folders¶

Each Truvari output directory contains benchmarking results comparing the SyRI structural variants against sequencing-based SV calls:

ref_x_modsyri_SampleName_sv_short_read_truvari/¶

Comparison between SyRI SVs and SVs called from Illumina short reads.

ref_x_modsyri_SampleName.pacbio_sv_long_read_truvari/¶

Comparison between SyRI SVs and SVs called from PacBio long reads.

ref_x_modsyri_SampleName.ont_sv_long_read_truvari/¶

Comparison between SyRI SVs and SVs called from Oxford Nanopore long reads.

Each Truvari output folder usually contains:

• Matched SV calls
• Unmatched (false negative / false positive) calls
• Precision, recall, and F1 scores
• Comparison summary statistics

Tools Used¶

The table below summarises all tools used within the pipeline:

Citation¶

• English, A.C., Menon, V.K., Gibbs, R.A. et al. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol 23, 271 (2022). https://doi.org/10.1186/s13059-022-02840-6

• Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

See Also¶

• Reference vs Modified Processing Pipeline - SyRI baseline variants
• Short-Read Processing Pipeline Results (Illumina) - Short-read SV calls
• Long-Read Processing Pipeline (PacBio & Oxford Nanopore) - Long-read SV calls