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

combine GVCF



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    I used GAYK/ 3 to combine multiple vcf files in the past, but it is no longer working. GenomeAnalysisTK -at 8 -T GenotypeGVCFs 

    Now, I tried to use this command to combine multiple vcf files. 

    gatk CombineGVCFs \

    Please let me know if the CombineGVCFs do the same thing as the past version. Thanks.

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    Genevieve Brandt (she/her)

    Hi Aziz,

    Yes, CombineGVCFs in GATK4 is the same as CombineGVCFs in GATK3, with a few bug fixes. The error you are getting here looks like it could be from a typo in your command line or an issue with permissions:

    A USER ERROR has occurred: Couldn't read file file:///scratch/brown/aebrahi/regia_ref2/carya/WG/SRR11497836.vcf.gz. Error was: It doesn't exist.

    Once you resolve the issue with the file, CombineGVCFs should work just fine.



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