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

picard CollectAlignmentSummaryMetrics required arguments format


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    Genevieve Brandt (she/her)

    Hi Serge,

    Thanks for writing into our forum! There are a couple things in your command that will cause issues and error messages:

    1. You are submitting filenames with curly braces ({}) and asterisks (*) which are not legal in our file system format. Because the filename is given in single quotes, the file names are read as-is (so the asterisk is read as a literal asterisk) and the file name is not found in your system.
    2. You cannot submit multiple input files this way for the input and output files. If you want to submit multiple files, you will either need to write out -I filename1.bam -I filename2.bam etc etc. Or, you can submit a .list file with a list of filenames. You can easily create the list using a bash command, so that would probably be the fastest option.

    Hope this helps your command run smoothly!



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