No records when merging vcfs from HaplotypeCaller and mpileup
I am using gatk MergeVcfs or bcftools isec to compare the vcfs from different pipelines (GATK4 HaplotypeCaller, SAMtools mpileup and DeepVariant).
However, when I tried to merge the gvcf from HaplotypeCaller with vcfs from other variant callers using bcftools isec, there is no records in the merged vcf file (or return " The contig entries in input file my.g.vcf are not compatible with the others." when using gatk MergeVcfs). I was wondering whether this is because there is in the ALT column. Can anyone tell me how can I further process the gvcfs from HaplotypeCaller to make it comparable with other vcfs?
Thanks for any suggestions!