Excuse me :
I used HC (haplotype caller) to call variants to create variant format file. The sample order in HC was not the same as that in variant format file. Was there any rule in that?
Many thanks in advance!
So, if you grep CHROM [yourvcf], are the samples in alphabetical order?
grep CHROM [yourvcf]
GATK sorts samples alphabetically; this is the expected behavior.