Does CombineGVCFs + GenotypeGVCFs software exist for gVCF files produced by Freebayes?
Since December 2015 Freebayes support gVCF files as output: https://github.com/ekg/freebayes/releases/tag/v1.0.2
It's now more than a year later and as far as I know still no software exists to merge Freebayes gVCF files in a "proper" way.
With proper gVCF merge I mean gVCF merge including re-calculating the variants and genotypes from the information available over the entire population of samples.
For GATK gVCF files CombineGVCF does the merge and then GenotypeGVCF recalculates the variants and genotypes.
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_CombineGVCFs.php
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php
I know DNAnexus is developing GLnexus for merging and genotyping freebayes gVCF files on demand. https://github.com/dnanexus-rnd/GLnexus
But I am not sure how close GLNexus is to a working production version and if their software will be available outside of DNAnexus cloud.
Is there other software available available or being developed that will be able to merge Freebayes gVCF files in a proper way?
There must be more Freebayes users (e.g. Sanger & EMBL/EBI) that would like to have an alternative to GATK for large incremental populations where gVCF is needed?
Maybe someone with the correct contacts could forward this question to Erik Garrison (Freebayes developer), Mike Lin (GLnexus developer) or people at Sanger & EMBL/EBI that do a lot of large variant calling analysis with Freebayes? Thank you.