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The microarray technology is an established approach for high throughput gene expression analysis. An accurate mapping between array probes and the genes that they are targeting is essential for generating accurate biological findings. The manufacturers typically provide such annotation tables. However, these tables rely on older genome and transcriptome versions that differ substantially from the current state-of-the-art sequence databases.
Re-Annotator is a re-annotation pipeline for gene expression microarrays that will bring probe annotations up-to-date!
The preprint of the paper describing Re-Annotator and its advantages is available at bioRxiv: http://biorxiv.org/content/early/2015/05/21/019596
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This is really an excellent tools for re-annotation, but could you inform me how to Use "BWA index" to generate the BWA index files for the exome reference sequence and the whole genome sequence data and how's the file hg19genome.fasta.gz comes from?