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Forgot to add -ERC GVCF when using haplotypecaller

Hi,
I have used the haplotypecaller to call the variants for my each sample without -ERC GVCF. Thus, I can not use the GenotypeGVCFs to merge them together. What should I do to resolve this problem? Should I re-run them? There are lot of samples. Although I can merge them together using bcftools, the result do not contain 0/0 type, there are only ./. 0/1 1/1 three types. I want to get a final merged VCf file which contain 0/0, ./., 0/1, 1/1
Can anyone help me?

Cheers,
Jian

Answers

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