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

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4 comments

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    dai

    Hello, Genevieve

     I have a question that I'm using gatk to call snp of my samples, but the organism has no known snp database, so I can't perform the BQSR. And I read some recommendation for it, mainly including 2 solution: ①just to skip the BQSR,②to create a confifent snp database and use it for BQSR. However, the latter will take much time as I have a big number of sample. So I want to skip the BQSR, meanwhile, use hard filtering instead of VQSR to get my finnal vcf. I just want to know whether this solution is  correct? and whether the information in final vcf file is credible if I perfoemed like this?

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    Muhammad Shoaib Akhtar

    Genevieve Brandt (she/her) I can't access form for GATK guru. It says you need permission. Please fix it.

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    Genevieve Brandt (she/her)

    Thanks for the heads up Muhammad Shoaib Akhtar! I think I fixed it, please let me know if it works.

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    Muhammad Shoaib Akhtar

    Genevieve Brandt (she/her) I'm sorry it didn't work. Following is error.

    You need permission

    This form can only be viewed by users in the owner's organization.

    Try contacting the owner of the form if you think this is a mistake. Learn More.

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