The reads are then mapped to the reference genome using the BWA-MEM algorithm (Langmead, Trapnell et al. 2009; Kim, Pertea et al. 2013).
The output BAM file is filtered to remove unmapped reads, unmapped mates, non-primary alignments and any read which has a mapping quality below 30. Only the reads that pass these filters are used for further analysis.
V3 Pipeline uses BWA from Sentieon®, which is concordant with the original BWA. Original BWA had a bug that resulted in an incorrect MAPQ for a small number of alignments which is fixed with Sentieon’s version.
Pipeline V2 uses the open source BWA for alignment.