Germline CNV vs HaplotypeCaller/indels
I have a question.
What is the difference in the indels called from haplotypecaller and germline CNV.
Is the deletion variant detected in haplotypeCaller has to be present in the vcf generated from germline CNV.
Im trying to validate the gCNV by comparing the deletion variant detected in vcf generated from haplotypeCaller and confirmed by sanger.
Is this a write process to say the gCNV results is correct or not
-
Hi Heba B abusamra, the GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, check out our support policy.
Please sign in to leave a comment.
1 comment