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

Question about the allele depth generated by haplotypecaller and ASEReadCounter


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    James Emery

    Hello. ASEReadCounter is an old tool part of our original RNA pipeline and it is not currently part of our RNA best practices so this tool should be considered use at your own risk. We do not have a set of recommendations for how best to run it under the conditions you have listed here. 

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