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You can obtain the truth VCF from!Synapse:syn2335185. To generate the compressed VCF file and its index:

$ bgzip -c data/truth.chr20.vcf > data/truth.chr20.vcf.gz
$ tabix -p vcf ../data/truth.chr20.vcf.gz

Scripts copied from Example invocation:

$ ./scripts/ -v data/truth.chr20.minus5plus2.vcf -t data/truth.chr20.vcf.gz -m SNV
tpcount, fpcount, subrecs, trurecs:
1440 2 1442 1445