Question: Sample order in vcf
0
gravatar for 897598644
4.6 years ago by
89759864480
China
89759864480 wrote:

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!

ADD COMMENTlink modified 4.5 years ago by Brice Sarver3.2k • written 4.6 years ago by 89759864480
0
gravatar for Brice Sarver
4.5 years ago by
Brice Sarver3.2k
United States
Brice Sarver3.2k wrote:

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

GATK sorts samples alphabetically; this is the expected behavior.

ADD COMMENTlink written 4.5 years ago by Brice Sarver3.2k
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