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Whole-genome sequencing in schizophrenia patients with low sequencing coverage

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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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slide1

Whole-genome sequencing in schizophrenia patients with low sequencing coverage

Kuang Lin

Department of Neuroscience

Institute of Psychiatry

Kings College London

slide2

A large cohort of schizophrenic patients

  • Extensive genetic, clinical and endophenotypic information
  • Employ low coverage whole genome sequencing to detect structural variants
why low coverage
Why low coverage?
  • ~1000€ per sample
  • ~500€ in two years.
  • Small files
easy to deal with
Easy to deal with
  • 100G fastq / sample, ~45G zipped
  • ~35G bam / sample
  • 50 x 5 hrs novoalign / sample
low coverage
Low coverage
  • ~400 million 100bp reads
  • FASTQC
  • Average depth ~13
slide6

FASTQC

  • Novoalign
  • samtools, PICARD tools
  • qualimap
  • GATK
slide7
3.5 million SNPs
  • ~0.5 million indels
acknowledgements
Acknowledgements

John Powell

Michelle Lupton

Stephen Newhouse