A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

Table 1

Alignment percentages for filtered reads and unfiltered reads. The average depth of coverage is for the alignment files created with the filtered reads.

Aligner	% reads aligned (unfiltered)	% reads aligned (filtered)	Average depth of coverage
Bowtie2	89.73	98.73	47.97
BWA mem	92.91	99.85	46.89
BWA sampe	85.95	97.49	46.67
CUSHAW3	85.00	99.81	47.69
MOSAIK	85.68	96.22	45.14
Novoalign	82.21	94.20	45.62