What happens to the genotype field in a g.vcf after CombineGVCFs

Question

[nhaus]

Hello,

I am using the joint germline variant calling approach to call germline variants. After running HaplotypeCaller on each sample, I combine them with CombineGVCFs. Everything works well and no errors occur. However, when I look at the resulting combined.cohort.g.vcf.gz I notice, that the GT field for ALL variants in both samples is just ./.. Before CombineVariants the GT field for the individual samples looked fine (0/1, 1/1,....).

Did anyone else experience this as well before and could explain me what it means? Or is this an expected behavior since no Errors were raised.

This is the exact command I used:

gatk CombineGVCFs -G StandardAnnotation -G AS_StandardAnnotation -R ref-genome.fa -V sample1.germline.merged.g.vcf.gz -V sample2.germline.merged.g.vcf.gz -O combined.cohort.g.vcf.gz

Any help is appreciated!

Cheers

Answer 1

[damian.loska]

Now you need something like:

java -jar gatk4.jar GenotypeGVCFs \
-R ref.fa \
-V combined.cohort.g.vcf.gz \
-O combined.cohort.vcf

cheers