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Count of A, C, G, T bases for each sample

Category Annotation Modules

VCF Field FORMAT (sample genotype-level)

Header definition line
  • FORMAT=<ID=BCS,Number=4,Type=Integer,Description="Counts of each base by sample">

  • Overview

    This annotation returns the counts of A, C, G, and T bases for each sample, in that order.



    This means the number of A bases seen is 3, the number of T bases seen is 0, the number of G bases seen is 3, and the number of T bases seen is 0.

    BaseCountsBySample is intended to provide insight into the pileup of bases used by HaplotypeCaller in the calling process, which may differ from the pileup observed in the original bam file because of the local realignment and additional filtering performed internally by HaplotypeCaller.


    • Can only be requested from HaplotypeCaller, not VariantAnnotator.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.