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

STAR and GATK RNAseq based SNP detection


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    Louis Bergelson


    This is a very late reply to this question, but maybe it's still useful.  I suspect what's happening here is that you are ending up with separating the fields in your header instead of tabs.  SAM header lines are TAB delimited, not whitespace delimited.  So either you accidentally used spaces instead of tabs in the headerline you specified or they were introduced somehow by STAR.  

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