Ococo: an online consensus caller

Motivation: The usual approach to variant calling from NGS data consists in inferring single nucleotide variants (SNVs) or more complex differences from read alignments. Consequently, variant calling is performed after all reads have been mapped to a reference genome and all read alignments are available. Existing variant callers usually operate by first sorting the alignments in increasing order of positions, and then sliding a small window through the genome and processing information collected within individual windows (read alignments, mapping qualities, base qualities). However, this approach is highly time- and space-demanding and all alignments must be available prior to variant calling. Results: We present OCOCO, the first online consensus caller, capable to infer SNVs dynamically as read alignments are fed in. OCOCO inputs unsorted alignments from an unsorted SAM/BAM stream and decides about single-nucleotide updates of the current genomic consensus using statistics stored in compact several-bits counters. Updates are reported in the online fashion using unsorted VCF. OCOCO provides a fast and memory-efficient alternative to the usual variant calling, particularly advantageous when reads are sequenced or mapped progressively, or when available computational resources are at a premium. Availability and implementation: OCOCO is available from http://github.com/karel- brinda/ococo.