Documentation

ChromosomeCounts

Counts and frequency of alleles in called genotypes

Category Variant Annotations

VCF Field INFO (variant-level)

Type StandardAnnotation, ActiveRegionBasedAnnotation

Header info
  • INFO=
  • INFO=
  • INFO=

  • Overview

    This annotation outputs the following:

    • Number of times each ALT allele is represented, in the same order as listed (AC)
    • Frequency of each ALT allele, in the same order as listed (AF)
    • Total number of alleles in called genotypes (AN)

    Example

    AC=1;AF=0.500;AN=2

    This set of annotations, relating to a heterozygous call(0/1) means there is 1 alternate allele in the genotype. The corresponding allele frequency is 0.5 because there is 1 alternate allele and 1 reference allele in the genotype. The total number of alleles in the genotype should be equivalent to the ploidy of the sample.


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    GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA