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
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