Erich-Hartm

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I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error. If you're getting an error can you please post the full message in this thread?

Thank you, sir. In fact , firstly I called SNP from both parents respectively, and then combined both parents vcf files to a integrate vcf file, I want to get...

I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error. If you're getting an error can you please post the full message in this thread?

This is part of my biSNP.vcf file, include the annotation and reference genome name. thanks! [example.vcf.gz](https://github.com/broadinstitute/gatk/files/8398391/example.vcf.gz)

I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error. If you're getting an error can you please post the full message in this thread?

@meganshand Thank you very much, sir, you mean that if l want to use ASEReadCounter of GATK4, I should use F1 hybrid's whole genome sequence to produce VCF file. Usually,...