Fig. 2.

Concordance/discordance with TIGRA assembled contigs for predicted calls from FreeBayes (pre- and post-ABRA), Pindel and Haplotype Caller. Indels within the ranges enabled by ABRA are evaluated (deletions up to 2000 bp and insertions up to the read length). The numbers in the figure represent a cutoff point for variant quality scores as reported in the respective caller’s VCF output. A small number of pre-ABRA deletions >30 bp and 0 pre-ABRA insertions >30 bp are called. FreeBayes currently does not use reads partially overlapping an insert as supporting evidence, which may impact post-ABRA sensitivity for longer insertions