Main report

Main report

This is the report generated by the sort option. TAPES main report contains all annotations present in the input annotated VCF file. Several other columns will be added depending on the options used with the sort option.

Added columns

• One column per sample containing the variant genotype (0/0, 0/1 or 1/1)
• WT count: The number of homozygous wild type (Ref/Ref) individuals
• Het count: The number of heterozygous (Ref/Alt) individuals
• Hom count: The number of homozygous variant (Alt/Alt) individuals
• PS2 column for each Trio (if --trio was used): the de-novo status of the specific variant
• Odds ratio: the odds ratio calculation (only if at least 2 individuals in the cohorts are affected by a variant)
• CI : confidence interval associated with the odds ratio (95%)
• p-value : p-value associated with the Odds ratio calculation
• PSV1_contrib / PS2_contrib / ... / BP7_contrib: the status of the associated ACMG criteria for this variant (0 or 1)
• Probability_Path: The probability that this variant is pathogenic
• Prediction_ACMG_tapes : the ACMG category assigned by TAPES