Sample order in vcf

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!

genome sequence next-gen-sequencing alignment

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updated 4.1 years ago by Ram

• written 11.3 years ago by 897598644

1 answer

So, if you grep CHROM [yourvcf], are the samples in alphabetical order?

GATK sorts samples alphabetically; this is the expected behavior.

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written 11.3 years ago by Brice Sarver

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