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

is it ok to apply BQSR and HaplotypeCaller to autosome noncoding region by -L by chromoosme?



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    Genevieve Brandt (she/her)

    Hi Shanshan,

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

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



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    Pamela Bretscher

    Hi Shanshan,

    Yes, you should be able to run BQSR and HaplotypeCaller over only specified interval lists. You can find more information about how to specify and use intervals here. You can see in the tool documentation that BQSR and HaplotypeCaller both allow you to specify the "-L" option to operate over only chosen intervals. I hope this is helpful and please let me know if you have any additional questions.

    Kind regards,


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