No records when merging vcfs from HaplotypeCaller and mpileup

Kong75Kong75 Member
edited August 10 in Ask the GATK team

Hi,

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!

Best,
Paul

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