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

(How to) Call common and rare germline copy number variants Follow

2 comments

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    Enrico Cocchi

    Is there any way to get the log2 output instead of the CN from PostprocessGermlineCNVCalls?

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    Calvin Hung

    Hi, I believe the *.tsv files in the tutorial_11684.tar.gz either from the GoogleDrive or from the FTP site are deprecated and cannot run through GermlineCNVCaller since GATK v4.1.x.x. I managed to hack the format and fixed it myself. You might want to update the tutorial files as well.

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