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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

Syntax for MergeGVCFs function resulting in "no positional argument is defined"



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    Gökalp Çelik

    Hi R O

    Your command line seems to be incomplete

    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6G -jar /gatk/gatk-package- MergeVcfs --INPUT --OUTPUT ERR194159-30x.hg38.g.vcf.gz

    There is no INPUT defined in the --INPUT section in the final executed command. 

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    R O

    Thanks for that catch! I supposed that there is something wrong with looping over beforehand that populates the list of VCfs so that there's nothing that gets merged in the end? Right now the example workflow intakes BAM's which I have checked are valid - and then iterates over a set of interval files - which is a zipped folder of one .BED file that I obtained

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