I am using the joint germline variant calling approach to call germline variants.
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
GT field for the individual samples looked fine (
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!