Aligning sequence from molecular inversion probes

ABSTRACT Summary Molecular inversion probes (MIP’s) allow efficient enrichment of genomic regions of interest for the purpose of targeted sequencing. To date, there is a paucity of simple-to-use software to align sequences derived from this method. Here, we describe a single program that performs mapping, arm removal, and deduplication before outputting alignments in SAM format. Availability bwa-mips is available at https://github.com/brentp/bwa-mips under the MIT license. Contact [email protected]