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

CollectReadCounts : Incompatible contigs Error


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    Gökalp Çelik

    Hi Vignesh Ravichandran

    CollectReadCounts requires a bam file and intervallist file to collect read counts from given intervals. Your command line does not show any bam inputs. Can you check that?

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