Total deletion calls and tool-specific deletion calls for each aligner and variant caller run with and without filtering.

The union of variant calls for each tool was calculated and false positive and false negative rates determined relative to high quality GIAB variants. Tool-specific calls were also calculated, defined as deletions specific to a single tool. aFrom bases overlap ENSEMBL v75 canonical transcripts. Total deletion calls and tool-specific deletion calls for each aligner and variant caller run with and without filtering.