Question: GATK Variant calling
0
gravatar for jaqx008
11 months ago by
jaqx00840
jaqx00840 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 • 558 views
ADD COMMENTlink modified 11 months ago by finswimmer8.0k • written 11 months ago by jaqx00840

this link can be helpful

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

ADD REPLYlink written 11 months ago by reza190

Thanks for sharing this link reza

ADD REPLYlink written 11 months ago by jaqx00840
0
gravatar for finswimmer
11 months ago by
finswimmer8.0k
Germany
finswimmer8.0k 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 11 months ago by finswimmer8.0k

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

ADD REPLYlink modified 11 months ago • written 11 months ago by jaqx00840
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1558 users visited in the last hour