Ultra deep targeted exome pipeline
ODESSA is a web tool to perform a Ultra deep targeted exome pipeline and provides easy access through interface to intermediate and final results.
The pipeline is composed of several steps:
- Verification of input integrity, quality checks, read trimming and primer contamination removal;
- Gapped alignment;
- BAM conversion, sorting and indexing;
- Duplicates removal, as they result as PCR amplification bias;
- A local realignment around known IN-DELs position, carried on to delete the other artifacts;
- Quality score recalibration to refine some oddness caused by sequencing and mapping on quality scores;
- Variants (SNP and DIP) calling from the filtered mapping data obtained from the previous steps;
- Association of as many annotation as possible to the variant list (i.e. annotation stored in database like dbSNP, 1000 Genomes Project, etc.);
- Data post processing: raw outputs are parsed and stored into custom databases to allow cross-linking and intersections, statistics and much more.
IEEE HPCS 2014. 07/2014; DOI: 10.1109/HPCSim.2014.6903743
ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data
Mattia D'Antonio, Paolo D'Onorio De Meo, Tiziana Castrignanò, Giovanni Erbacci, Matteo Pallocca and Graziano Pesole
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