GATK Variant calling
Hello everyone. Does anybody has a protocol to call SNPs with the GATK pipeline? and a brief explanation on what is what would be especially helpful as this would be my first time doing variant discovery. Thanks in anticipation
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jaqx008
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Hello,
as always the answer to such an open question is: "It depends" :)
Maybe you can start with GATK's Best Practices Guide or have a look at the documentation of the HaplotypeCaller, which is the recommended tool for Variant Calling with GATK.
fin swimmer
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this link can be helpful
https://gencore.bio.nyu.edu/variant-calling-pipeline/
Thanks for sharing this link reza
In case anyone stumbles upon this post, and updated version of the pipeline linked to above, using GATK4, is available here: https://gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/