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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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

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    Pamela Bretscher

    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

    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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