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Identifying sequence variants in ordered SAM files

AgileAnnotator identifies sequence variants that repeatedly occur in reads that have previously been aligned to a reference sequence by an alignment program, such as BWA or Novoalign, and exported as SAM files. For AgileAnnotator to work correctly, the sequence reads in the SAM file must be ordered by chromosome and chromosomal position, which can be done using AgileSamFileSorter.

AgileAnnotator identifies sequence variants that ae either in protein-coding exons or within 50 bp of an exon’s splice sites. Sequence variants outside of these regions are ignored and so AgileAnnotator is primarily designed to analyse sequence data derived from exome pulldown experiments.

Guide to use of AgileAnnotator:

The AgileAnnotator user guide can be found here.


The AgileAnnotator program can be downloaded from my department web site here.

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