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

How to combine GVCFs annotated by b37 (decoy) and hg19 reference genomes?

michellelianmichellelian SingaporeMember
edited March 1 in Ask the GATK team

Hi GATK team,

We have 2 GVCFs WES datasets. a) GVCFs ran using HaplotypeCaller with b37 decoy, b) GVCfs ran using HaplotypeCaller with hg19. We plan to combine all the GVCFs into 1 Master VCF, by doing a CombineGVCF (in batches) then GenotypeGVCF.

Am wondering if it is recommended to do a liftover of GVCFs dataset (a) to hg19, using the b37tohg19 chain file ( Will there be any issues doing this liftover? Else are there any alternatives we could try to combine both GVCFs datasets?

Thank you so much for the kind help and advice.


Best Answer


Sign In or Register to comment.