truvari.md

Truvari Tutorial

Install

mamba create -n truvari python=3.7
python3 -m pip install truvari

Introduction

Truvari is a command-line toolkit for structural variant (SV) comparison. It's used for benchmarking SVs against a known reference, merging SV calls, and annotating differences.

Preparing Data

Ensure your VCF files are bgzipped, sorted, and indexed. Here's how you can prepare your data:

# Compress VCF file
bgzip -c input.vcf > input.vcf.gz

# Sort the compressed VCF
bcftools sort input.vcf.gz -Oz -o sorted_input.vcf.gz

# Index the sorted VCF
tabix -p vcf sorted_input.vcf.gz

Benchmarking SVs

To benchmark SVs, use the truvari bench command:

# Running Truvari benchmarking
truvari bench -b sorted_svim_example.vcf.gz  -c sorted_pbsv.vcf.gz -o truvari_output/ --reference GRCh38.p13.genome.fa

truvari bench -b base.vcf.gz -c comp.vcf.gz -o output_directory

Replace base.vcf.gz with your reference VCF file and comp.vcf.gz with the VCF file you want to compare.

Results

After running the benchmarking, Truvari will generate an output_directory containing:

• summary.txt: A summary of the stats between the base and comparison.
• tp-base.vcf.gz and tp-call.vcf.gz: True positives from the base and call sets.
• fn.vcf.gz: False negatives.
• fp.vcf.gz: False positives.

To check the results, you can look into summary.json:

cat output_directory/summary.json

Advanced Options

Truvari has several advanced options for fine-tuning the comparison, such as adjusting size filters and match criteria. Consult the official Truvari documentation for detailed usage and examples.