Given RNA, DNA and/or hybrid (mixture) genome sequence samples-as supported by NCBI's ENA - NGSEP can map reads back to the reference genome (for RNA) and variants in genes using GATK.
Given a variation call - NGSEP can detect variations contained within the variant call format (VCF) and annotation using GATK.
Visualize sequence alignments and variants in real time, view statistics, annotate variants, perform sequence 6add127376 rebbroo
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