VCF2CNA

St. Jude Children's Research Hospital
St. Jude Research

Efficiently detect Copy number Alteration

Obtain Copy number Alteration from VCF, MAF, or Bambino formatted genotype data

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Default Parameter Specifications

  • Specify Diploid Chromosome: Normalize results to specified chromosome
  • Median Normal Coverage: Median coverage value of SNPS from normal samples
  • Minimum Scale Factor (autosomes): This value is multiplied by the median to compute the minimum coverage value
  • Maximum Scale Factor (autosomes): This value is multiplied by the median to compute the maximum coverage value
  • Minimum X Scale Factor: Minimum scale factor for chromosome X.
  • Maximum X Scale Factor: Maximum scale factor for chromosome X.
  • Sample Order (VCF Format Only): VCF input must include Tumor and Normal data following the FORMAT Field. Tumor/Normal assigns the Tumor data to the 1st field following FORMAT and Normal data to the 2nd field following FORMAT. Normal/Tumor is inverse.

VCF2CNA App

Select Delivery Method

Specify Diploid Chromosome
Median Normal Coverage
Minimum Scale Factor
Maximum Scale Factor
Minimum X Scale Factor
Maximum X Scale Factor

Sample Order [VCF Format Only]

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