PT - JOURNAL ARTICLE AU - Brent S. Pedersen AU - Elissa Murphy AU - Ivana V. Yang AU - David A. Schwartz TI - Aligning sequence from molecular inversion probes AID - 10.1101/007260 DP - 2014 Jan 01 TA - bioRxiv PG - 007260 4099 - http://biorxiv.org/content/early/2014/07/19/007260.short 4100 - http://biorxiv.org/content/early/2014/07/19/007260.full AB - 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