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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

BaseRecalibrator tool recalibration table


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    Genevieve Brandt (she/her)

    Hi Sharon Natasha Cox,

    Thanks for writing into the GATK forum! Let's see if we can figure out if there is something wrong here. 

    It's normal that your recalibration tables should be similar/the same size but the tables should have different contents. You could run a diff command between the files to verify that the contents are different.

    You can also run the tool AnalyzeCovariates to analyze your recalibration tables to determine if there were issues during BQSR:

    I did notice that there was potentially a typo in your output variable, so you might want to check your command:  -O Recal_data110_manua,table.

    Let me know if you have any questions.



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