Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

limitation in command length

naarkhoonaarkhoo Posts: 37Member

I wonder if there is any limitation for the command length. I provide more than 90 bam files, including their directory address to GATK for variant calling using UnifiedGenotyper, and it seems it doesn't parse whole the command. I know It could be because of java, also. Have you ever experiences similar problem ? Is there any way to provide a directory path instead of all single bam files path as the input ? thanks,

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