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

SelectVariants and Hard Filtering order changes final number of variants?


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    Gökalp Çelik


    Did you observe any variant sites to be lost in the reversed order? Normally multisample VCF also contains non-variant sites for your sample of interest therefore if your filtration or selection involves removal of non-variant sites observing different numbers could be understandable. Can you check if a particular variant site being lost in one or the other method and can you post it here?


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