rtgeval: A Shell repository from lh3

Getting Started

wget -O- https://github.com/lh3/rtgeval/releases/download/v0.1/rtgevalkit-0.1_x64-linux.tar.bz2 | tar -jxf -
[ -d ref.sdf ] || rtgeval.kit/rtg format -o ref.sdf ref.fa  # create RTG index
rtgeval.kit/run-eval -s ref.sdf -b confident.bed truth.vcf.gz test.vcf.gz
cat test.re.eval

where confident.bed gives confident regions, truth.vcf.gz the truth VCF and test.vcf.gz the VCF to evaluate. test.re.eval gives the true positives (TP), false negatives (FN) and false positives (FP) measured in three ways, which will be explained below.

For the CHM1-CHM13 benchmark data, it is recommended to invoke rtgeval with

rtgeval.kit/run-eval -s ref.sdf -b conf.bed -l2 -L100 -h hrun.bed truth.vcf test.vcf

This ignores 1bp INDELs and homopolymer INDELs.

Introduction

This repo implements a wrapper for RTG's vcfeval, a sophisticated open source variant comparison tool developed by Realtime Genomics. It simplifies the use of vcfeval and potentially helps to get consistent results given VCFs produced by different variant callers.

The wrapper calls bgt to decompose complex and multi-allelic variants to the smallest possible alleles, optionally filters each allele and regroups overlapping multi-alleles into one VCF line (apparently rtg vcfeval works better this way). The wrapper then calls hapdip and rtg to perform three types of evaluations:

Positional. With this approach, a TN is a true variant that is within 10bp around a called variant; a FN is a true variant that is not within 10bp; a FP is a called variant that is not within 10bp around a true variant. FN and FP intervals can be found in PREFIX.de-fnp.bed.gz.
Allelic. The wrapper calls rtg vcfeval --squash-ploidy. For biallelic variants, this type of evaluation measures if an allele from one VCF is confirmed in the other VCF, disregarding genotypes. The behavior for multi-allelic variants is unclear. FN and FP calls are reported in PREFIX.vea/f?.vcf.gz.
Genotypic. The wrapper calls rtg vcfeval. Genotype errors are also counted. This is the most stringent type of evaluation. False calls are reported in PREFIX.veg/f?.vcf.gz.