Question: GATK Variant calling
0
gravatar for jaqx008
2.4 years ago by
jaqx00870
jaqx00870 wrote:

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

snps gatk variant calling • 1.6k views
ADD COMMENTlink modified 2.4 years ago by finswimmer13k • written 2.4 years ago by jaqx00870

this link can be helpful

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

ADD REPLYlink written 2.4 years ago by reza220

Thanks for sharing this link reza

ADD REPLYlink written 2.4 years ago by jaqx00870

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/

ADD REPLYlink written 8 weeks ago by mk563610
1
gravatar for finswimmer
2.4 years ago by
finswimmer13k
Germany
finswimmer13k wrote:

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

ADD COMMENTlink written 2.4 years ago by finswimmer13k

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by jaqx00870
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