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Old 11-26-2013, 12:46 PM   #6
m_two
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Location: USA

Join Date: Mar 2010
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Another tool you may be interested in: https://github.com/ckandoth/vcf2maf

It uses snpEff to annotate all overlapping transcripts for each variant then filters the annotation to identify a single, best transcript isoform with the most severe effect and longest coding sequence.

The prioritization considers transcript biotypes and attempts to avoid pseudogenes and incomplete ORFs.
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