We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

HaplotypeCaller vs GCF->GenotypeGVCFs workflow for small WES cohorts

For small WES (whole exome) cohorts such as trios, is it better to:
a) Do HaplotypeCaller jointly on the trio exome BAM files
b) Do HaplotypeCaller on each individual WES BAM file individually in GVCF mode, followed by CombineGVCFs, followed by GenotypeGVCFs?

Or... do (a) and (b) produce equivalent results?

I'm assuming that the computational resources difference between (a) and (b) is not significant enough to warrant deciding on anything other than purely best accuracy (i.e. sensitivity and specificity).


Sign In or Register to comment.