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Whole-genome sequencing in schizophrenia patients with low sequencing coverage

Whole-genome sequencing in schizophrenia patients with low sequencing coverage. Kuang Lin Department of Neuroscience Institute of Psychiatry Kings College London. A large cohort of schizophrenic patients Extensive genetic, clinical and endophenotypic information

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Whole-genome sequencing in schizophrenia patients with low sequencing coverage

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  1. Whole-genome sequencing in schizophrenia patients with low sequencing coverage Kuang Lin Department of Neuroscience Institute of Psychiatry Kings College London

  2. A large cohort of schizophrenic patients • Extensive genetic, clinical and endophenotypic information • Employ low coverage whole genome sequencing to detect structural variants

  3. Why low coverage? • ~1000€ per sample • ~500€ in two years. • Small files

  4. Easy to deal with • 100G fastq / sample, ~45G zipped • ~35G bam / sample • 50 x 5 hrs novoalign / sample

  5. Low coverage • ~400 million 100bp reads • FASTQC • Average depth ~13

  6. FASTQC • Novoalign • samtools, PICARD tools • qualimap • GATK

  7. 3.5 million SNPs • ~0.5 million indels

  8. Acknowledgements John Powell Michelle Lupton Stephen Newhouse

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