Version 5 (modified by Patrick Deelen, 13 years ago) (diff)


Compare Sequence Data With Genotype Chip

Status: Alpha Authors: Patrick Deelen, Morris Swertz

Tool to compare sequence data with data from genotyping chips.


  • Overview of concordance per sample
  • Matrix of all sequence samples vs all genotype samples
    • This is used to detected sample mix-ups
  • Performance per SNP


The genotype data input is currently PED/MAP as generated by plink.

Both QCed as non QCed data is supported. The following sequence file formates are supported

  • VCF
  • Q20 (as provided by BGI)
  • CNS


  • Plots to give more insight in SNP performance

Attachments (6)

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