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

FastqToSam (Picard) Follow


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    Christian Butera

    I am using docker on windows with the latest gatk installed. I am getting errors like this:

    no main manifest attribute, in picard.jar


    Error: Unable to access jarfile picard.jar



    Where can I find out how to fix these issues while I try to use FastqToSam?

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    Esteban Peguero Sanchez

    I assume that the syntax in the case of pair-end and using the option --USE_SEQUENTIAL_FASTQS would be something like:


    RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R2_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R2_002.fastq

    would that be correct?

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