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One sample analysis with HaplotypeCaller
I was wondering if this will give the same results for a ONE sample analysis:
A ) HaplotypeCaller in GVCF mode and then GenotypeGVCFs to get a normal vcf file instead of the g.vcf for just the one sample
B ) HaplotypeCaller in normal mode for just the one sample
Which one is the recommended route for a one sample analysis?
Thank you for your help!!!