GATK Variant calling

Question

[jaqx008]

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

[reza]

this link can be helpful

https://gencore.bio.nyu.edu/variant-calling-pipeline/

[jaqx008]

Thanks for sharing this link reza

[mk5636]

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/

Answer 1

[finswimmer]

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

[jaqx008]

Thank you. I will look at that, and add question when an error I can't resolve comes up