Question: GATK Variant calling
0
gravatar for jaqx008
5 months ago by
jaqx00830
jaqx00830 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 • 263 views
ADD COMMENTlink modified 5 months ago by finswimmer2.7k • written 5 months ago by jaqx00830

this link can be helpful

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

ADD REPLYlink written 5 months ago by reza190

Thanks for sharing this link reza

ADD REPLYlink written 5 months ago by jaqx00830
0
gravatar for finswimmer
5 months ago by
finswimmer2.7k
Germany
finswimmer2.7k 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 5 months ago by finswimmer2.7k

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

ADD REPLYlink modified 5 months ago • written 5 months ago by jaqx00830
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