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

FastaAlternateReferenceMaker generates same sequence for multisample vcf


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    Giles Hall

    I am sorry for the trouble you are having getting your variants to merge with your reference.  Based on the log file and your invocation, it would seem that the method executed successfully in spite of there being no change to the sequence in your output file.  In order to further assist you, would you please attach a similar log showing how you invoked SelectVariants, and its subsequent output?  Thanks.

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