I executed HaplotypeCaller and GenomicDBimport (GATK version 184.108.40.206).
In my haplotypeCaller results (sample names = 2016000051),
there is no variant on chr1:10363 as below.
However, when I merge all samples using GenomicDBImport & Genotyping,
I had this result.
How emit this result?
In this vcf, what mean this star?
I find the variant on chr1:10120 T>A as below.
But, consolidate vcf dosn't have this variant. I can't understand.
In my haplotype calls, they emit the genotype on chr1:10126 as below.
But in my consolidate vcf,
the genotype is "./.".
And the DP (107) is also different with haplotype caller vcf (DP=122).
In my HaplotypeCaller gvcf,
In my consolidate vcf,
How can emit the genotype (2|2) on chr1:10177??
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