To help you get how to make effective use of AnnotSV, we have provided an input/output example set using the HG00096 individual data from the 1000 Genomes project (phase 3) (Sudmant et al. An integrated map of structural variation in 2,504 human genomes. Nature. Oct 2015).

- The HG00096 SV input file (HG00096.SV.bed) comprises 4,751 SV ranging in size from 50 bp to 1.2 Mb.
- The HG00096 SNV/indel input files (HG00096.chr*.phase3.vcf) contain 4,194,572 variants.

$ANNOTSV/bin/AnnotSV -SVinputFile HG00096.SV.bed -snvIndelFiles "HG00096.chr*phase3.vcf" -outputFile ../Output/HG00096.SV.annotated.tsv -svtBEDcol 4 -SVinputInfo 1 -genomeBuild GRCh37

The results are available in the HG00096.SV.annotated.tsv file