Genome Analysis Toolkit

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

Combine two panel-of-normals files



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    Philipp Hähnel

    Hi Robin,

    you can use MergeVcfs for merging the two PoN vcfs:

    gatk MergeVcfs -I pon1.vcf.gz -I pon2.vcf.gz -O merged_pon.vcf.gz



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    Steffen Møller Bøttger

    This does seem to work. But according to MergeVcfs:

    If there are samples, those must be the same across all input files.

    I have successfully run it with one VCF with samples and one without, so the requirement is not strict, it seems.

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