Alignment and analysis pipeline for NHS targeted sequencing
Only for historical interest. Original Bash pipeline for Exeter Molecular Genetics Lab circa 2012-2013
GATK Best practices pipeline with hard filtering on a given common sequencing artefacts and variants of no known clinical signficance. Since superceded by a Ruby based pipeline (after 2013).
Capture number,MODY number,EX number,Gender,Analysis,Disease,Sample type,Comment
p5_8_001,MY0000XX01,EX0000001,Male,MODY,MODY,Whole blood,positive control (1) HNF1A c.872dup/N
p5_8_002,MY0000YY02,EX0000003,Female,MODY,MODY,Whole blood,positive control (2) HNF1B delex1-9/N
Copyright (C) 2013 Garan Jones
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