Computational protocol: Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness

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Protocol publication

[…] Two hb/hb were used for whole genome sequencing. Sequencing was performed using Illumina Genome Analyzer II platform as paired-ends 100-bp reads according to the manufacturer's protocol. Four lanes of sequence were generated for each mouse. Sequences were mapped to the reference genome (NCBIm37) using bwa0.5.9 and were improved by local realignment around insertions and deletions discovered in the mouse genomes project using GATK 1.1–5 . The lanes were merged and library duplicate fragments were marked using picard (http://picard.sourceforge.net, version 1.47. Accessed 2012 Aug 2.) and the merged BAM files were analysed using the Integrative Genomics Viewer (IGV) software . Sequence data have been deposited in the European Nucleotide Archive (accession number: ERP000977). […]

Pipeline specifications

Software tools BWA, GATK, Picard, IGV
Application WGS analysis
Organisms Mus musculus, Homo sapiens
Diseases Vestibular Diseases