Supplementary data for “Benchmarking short-read germline structural variant calling highlights advantages of using ensembles of tools and small impact of graph genome alignment”

This repository contains the supplementary data for the paper titled “Benchmarking short-read germline structural variant calling highlights advantages of using ensembles of tools and small impact of graph genome alignment”.

Per-sample (eg NA12878) and per alignment (eg graph vs linear) folders containing:
– VCF output (both pre-processing (eg linear-Smoove-NA12878.vcf.gz) and post-processing (linear-Smoove-NA12878.final.vcf.gz))
– Truvari type-ignore standard output (fp.vcf.gz, fn, tp-comp, tp-base, summary.json)
Bam used for NA12878 graph:2188.v4.2.4.grc38_HPRCv1X.bam