Ambiguity in genetic data file | Sequencing.com

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Ambiguity in genetic data file

This alert appears when the genetic data file used to generate this report. To overcome this ambiguity, the analysis used to generate this report had make assumptions about the data and these assumptions may not be accurate. 

 

Technical information

  • The analysis used to generate this report made the following assumption: the genotype for all chromosomal coordinates not included in the genetic data file are the same as the reference genome.
  • The VCF file used to generate this report only included data for a chromosomal coordinate if the variant (alt) allele was detected.
  • The VCF file did not include any data for a chromosomal coordinate if the result was either a no-call or the same call as the reference genome.
    • Because no-calls are excluded from the file and some of the no-calls may be alt, assuming all chromosomal coordinates not included in the data are ref may be incorrect.
    • This only applies to chromosomal coordinate data that was not included in the VCF file. All chromosomal coordinate data that was included in the file was analyzed without any assumptions having to be made.

 

Avoiding ambiguity

  • The best way to avoid ambiguity is to avoid using the standard VCF format.
  • Ambiguity can be overcome if the genetic data is in one of the following formats: CRAM, FASTQ, FASTA, BAM or SAM formats.
    • If you have one of these files, use one of these files instead of a VCF format as the starting file for apps that conduct genetic analysis (such as the Wellness & Longevity app).
      • Sequencing.com will automatically process these files in such a way as to avoid the ambiguity that may otherwise exist with VCF format.
    • You may also use the EvE app to convert one of those file formats into a clinical+ VCF file.
      • This format avoids the ambiguity of the regular VCF format.
      • You can then use the clinical+ VCF file as the starting file for an app.