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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    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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