Not enough individuals in the file

[annyyj]

Not enough individuals in the file

[magnusdv]

Hi,
Are all 12 individuals in the same file, or do your have one file for each trio?
In any case, could you share the top part of a variant file that is giving you strange results? Including a few of the variant lines, please. The error message suggests that there may be formatting issues, but I would need a look at the data to say for sure.

[annyyj]

github.zip

Hi，
I have one file for each trio，I used GATK to convert three gvcfs to one vcf.
There are 4 files in the package, first 500 lines from variant files
one trio get correct result : Get_the_right_result.vcf
three trios have empty results: no_result_*.vcf
Best wishes.