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Too much varients
We did exome sequencing to one person and run it through GATK best practice pipeline (used Haplotype Caller) combined with 10 samples which I have downloaded from 1000 Genomes project (as recommended). It's Appear that my sample have around 450,000~ SNVs. Is it normal result??
We also analyzed this sample using BGI(china) services (not sure which pipeline they have used, unfortunately) and we VCF file with only 35,000 SNVs..
Is there a problem my analysis?