To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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?

Answers

Sign In or Register to comment.