No GT field in merged vcf file

[yangyxt]

I just tried to merge vcf files separately from gridss, delly and pindel and found that no GT field is in the merged vcf file.

The command I ran is:
mergeSVvcf -l gridss,delly,pindel -o merged.vcf gridss.vcf delly.vcf pindel.vcf

Not only I cant find a field named GT in FORMAT, but also I cant find a inherited GT field like gridss_GT or delly_GT.

Does mergeSVvcf consider normalizing GT info ? Or does mergeSVvcf just quit normalizing this info?

Thanks!

[yangyxt]

If the issue above is a choice instead of a bug for mergeSVvcf, it just so painful to see this...Seems the GT info from all callers, which is intensively needed for downstream analysis, is completely discarded during the merging process.