Does anyone know a recent comparison done of the BWA-mem and Berkeley SNAP aligner?
Especially if it leads to similar True Postive (TP), True Negative (TN) variant call ratios for snp, indel, complex and structural variants. (by variant calling the BAM files produced by BWA and SNAP using GATK/ Freebayes and structural variant callers).
Also it would be nice if the actual speed was compared between BWA-mem and SNAP in the comparison.
The authors of SNAP claim "that it is 3-20x faster and just as accurate as existing tools like BWA-mem".
See also this presentation:
SNAP would be a good alternative to bwa-mem if someone could independently confirm these precision, recall and speed numbers, for human and maybe a second non human genome.