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GenotypeGVCFs on one sample

mayaabmayaab IsraelMember ✭✭

Hi GATK team,

In the documentation of GenotypeGVCFs it is writen:
"Input - One or more Haplotype Caller gVCFs to genotype"
I have 3 questions regarding this tool:
1. I wonder, what is the meaning of running it on one sample?
2. I tried to run it on one sample, and noticed that the genotype quality is different than the one in the original gvcf file from HC. What is causing this difference? I'm asking this since running the tool on one sample means that there are no other samples to consider in recalculating the quality.
3. Last question - From your experience, what is the best way to analyze one exome sample? Should I run HC with the default genotype_mode parameter and do hard filtering? Should I run HC in GVCF mode, run GenotypeGVCFs and than do hard filtering? Any other suggestion?

Thank you for the answer,
Maya

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