3.8. JCNVv1

Dataset category

Copy Number Variation

Summary

Copy number variation data obtained from short-read whole genome sequencing of 48,874 Japanese individuals

References

  • Tadaka et al. [2]

Samples analyzed

Blood (buffy coat), saliva

Analysis method

  1. Perform following procedure to CRAM files that created by 54KJPN-SNV/INDEL

  2. Randomly select 200 samples for each sequencer and sequencing institution combination

  3. Run the GATK CNV Germline Cohort Workflow for each set of 200 samples selected in step 2.

    • At this time, the CNV analysis bin is based on the non-N region of each chromosome cut every 1 kbp

  4. Group all samples by 200 samples for each sequencer and sequencing institution combination

  5. Run the GATK CNV Germline Case Workflow for each group created in step 4 using the Panel of Normal created in step 2.

  6. Count the number of amplification regions and loss regions for all autosomes in the sample prepared in step 5.

  7. Use Inter-Quartile Range (IQR) to remove samples with outliers in amplification and loss counts

    • 1.5 times the IQR added to 75percentile as the upper limit and 1.5 times the IQR subtracted from 25percentile as the lower limit

  8. Remove samples selected in step 7 that are not included in 54KJPN-SNV/INDEL.

  9. Calculate the number of samples per CN per bin

Related pages on the jMorp website