Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification.
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Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R.
PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402