I am working on a classic variant calling on a non model organism.
I have 250 samples and followed the GATK best practice.
I have produced 250 g.vcf with HaplotypeCaller, now the next step is to combine those g.vcf and produce a .vcf (with GenotypeGVCFs) either:
A) Solution A: using GenomicsDBImport
B) Solution B: using CombineGVCFs
But those methods are super slow.
I am wondering if it is possible to produce one vcf per g.vcf with GenotypeGVCFs (quite fast) and then combine the 250 vcf with an another program ?
Does it produce the same result ? Thanks.