Sample order in vcf
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9.7 years ago
897598644 ▴ 100

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 • 3.1k views
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Entering edit mode
9.6 years ago
Brice Sarver ★ 3.8k

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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