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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 (https://github.com/broadgsa/gatk/tree/master/public/chainFiles)? 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.

-michelle

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