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

CombineGVCFs: How to sort the sample ID of the gvcf file header in combining gvcfs ?



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    Laura Gauthier

    Hi Senwei,

    The VCF spec doesn't specify sample ordering and the GATK convention is to alphabetize samples.  There is no way to change this ordering so you'll have to modify your analysis.  You may find SelectVariants with the sample name (-sn) argument useful.

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    Thank you very much

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