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

Missing ReadPosRankSum, MQRankSum and BaseQRankSum Scores in VCF

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    Genevieve Brandt (she/her)

    Hi Hamza Umut Karakurt, could you clarify this information:

    • How was the VCF file obtained? Was it with GATK?
    • Is there an issue with BQSR, since you supplied the commands above?
    • Which specific version of GATK4 are you using?
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