TY - JOUR T1 - Aligning sequence from molecular inversion probes JF - bioRxiv DO - 10.1101/007260 SP - 007260 AU - Brent S. Pedersen AU - Elissa Murphy AU - Ivana V. Yang AU - David A. Schwartz Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/07/19/007260.abstract N2 - 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 bpederse{at}gmail.com ER -