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

Struggling to assign read groups with AddOrReplaceReadgroups



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    Gökalp Çelik

    Hi Cora Olpe

    Since single sample runs work fine but in a loop you are getting this error this is most likely not a GATK problem but a GNU tool read issue. It is possible that the line ending char \n or \r\n are getting in the way of SM when it is read from the stream. Is it possible for you to add another character seperated by tab to each line after SM column and try again? Alternatively you may add a middle step to trim whitespaces or line ending characters at each line as cat reads the file. 

    I hope this works for you. 

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    Cora Olpe

    Hi Gökalp Celik,


    thanks so much, the extra character with tab solved it!


    best wishes


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