HaplotypeCaller to report read depth by strand and allele (SAC)

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Welliton de Souza

• November 24, 2021 18:21

Is it possible to annotate SAC (Number of reads on the forward and reverse strand supporting each allele (including reference)), using GATK 4 HaplotypeCaller? The FORMAT/SB does not provide read depth for each alternate allele.

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  Pamela Bretscher

  • November 26, 2021 15:25

  Hi Welliton de Souza,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Pamela

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  Pamela Bretscher

  • November 29, 2021 18:37

  Hi Welliton de Souza,

  I believe you should be able to find what you are looking for in the per-sample columns at the end of your VCF. The read depth for each reference and alternate allele should be separated by commas in the Allele Depth column of the VCF. Is this not what you are looking for?

  Kind regards,

  Pamela

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