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

Using GenomicsDB with intervals



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    Bhanu Gandham

    Hi ,

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    Jay Ross

    You can run GenomicsDBimport per chromosome, or on intervals smaller than whole chromosomes (I use an intervals list split anywhere there are consecutive N's in the reference genome). This will create a number of genomicDBs, which can then be genotyped into VCF files using GenotypeGVCFs. If all of the genomicsDB and VCF files have the same samples, you can then combine all VCF files into one final VCF using GatherVCFs.

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