Parallel alignment using MOSAIK

[iskandr]

Hi @wanpinglee,

I was curious whether the alignments produced by MOSAIK are completely independent across reads. For example, is it OK to run

MosaikAligner -in x.mkb -out x.mka -ia ref.dat -j ref_15 -annpe pe.ann -annse se.ann
MosaikAligner -in y.mkb -out y.mka -ia ref.dat -j ref_15 -annpe pe.ann -annse se.ann

and then merge x.mka.bam and y.mka.bam?

Would this give the same results as if we first concatenated the original x_R1.fastq + y_R1.fastq and x_R2.fastq + y_R2.fastq, and then aligned them together with a single call to MosaikAligner?