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

multiple vcf files in FastaAlternateReferenceMaker

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    Tiffany Miller

    Hi mk , my guess it the tool doesn't allow you to pass multiple files. Can you try merging your vcfs using MergeVcfs, then passing that output?

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    mk

    Hi Tiffany, thank you for your reply. I ended up using gatk CombineVariants to merge the vcfs (before posting this, just wanted to see if there was a way to do this using FastaAlternateReferenceMaker)

    Is there a difference between CombineVariants and MergeVcfs?

     

     

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    Tiffany Miller

    No problem! CombineVariants is not in GATK4 and hasn't been ported over because it's got to be fixed up. MergeVCFs is meant to do the same thing. That being said, if your files were merged correctly using the older tool, I think you are good to go. 

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