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What is a good number of samples that can be used to detect a variant - I have 15K GVCFs with 1000DP

ravichavravichav United StatesMember
edited December 2017 in Ask the GATK team

Hi,

I have 15k GVCFs. To call variants, I understand I can run combineGVCFs step to get batches of GVCF combined. I would like to know whats the good number for a sample set, for bams with coverage of over 800-1000X, to detect a variant? Would the variants called from batches of 500 samples have the same power to detect a variant in all the samples as compared to a variant call in 15k samples together?

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