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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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

  • Employ low coverage whole genome sequencing to detect structural variants


Why low coverage?

  • ~1000€ per sample

  • ~500€ in two years.

  • Small files


Easy to deal with

  • 100G fastq / sample, ~45G zipped

  • ~35G bam / sample

  • 50 x 5 hrs novoalign / sample


Low coverage

  • ~400 million 100bp reads

  • FASTQC

  • Average depth ~13


  • FASTQC

  • Novoalign

  • samtools, PICARD tools

  • qualimap

  • GATK


  • 3.5 million SNPs

  • ~0.5 million indels


Acknowledgements

John Powell

Michelle Lupton

Stephen Newhouse


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