limitation in command length

naarkhoonaarkhoo Posts: 38Member

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 ?

Best Answer


  • naarkhoonaarkhoo Posts: 38Member

    I don't know if it is relevant but it complains about un-index bam files.
    Should all bai files (indeces) located in the same directory ? is there option to set the path of bai files also?

  • naarkhoonaarkhoo Posts: 38Member

    Or to know which of the listed BAM files is not index-ed

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,737Administrator, GATK Dev admin

    Yes, the bai file indices should be in the same directory as the bams they index. There is no option to provide separate paths for the bam and bai.

    Geraldine Van der Auwera, PhD

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