REQUIRED for all errors and issues:
a) GATK version used: GATK 4.3.0
b) Exact command used: I used the command stated on gatk4.3.0 without any modifications and I combine and genotyped my vcf files. When I check the VCF file after haplotype caller, combing and genotyping of all vcf files, the SNP ID for all samples in all CHROM was missing and indicated by '.' I try to use variant annotator still, it doesn't work for me. I would appreciate if you share me your experience to solve such problem.
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