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CatVariants mis-sorting input VCFs

GATK Team,

When using CatVariants on my data, I noticed that it was consistently mis-sorting the output (when not using --assumeSorted; in my case, using the --assumeSorted is not feasible as the input VCFs are not ordered). Looking at the code, it appears that CatVariants is sorting the output files based on the position of the first variant in the VCF file, which can potentially lead to strange behavior. As an example, assume we have the following 3 VCF files to concatenate:

#CHROM  POS
1       10
#CHROM  POS
1       30
#CHROM  POS
2       20

Without the --assumeSorted option, CatVariants would output

#CHROM  POS
1       10
2       20
1       30

I've attempted a fix for the issue by using the VariantContext of the first variant instead of the position (null VariantContext in the case of assumeSorted) here: https://github.com/broadgsa/gatk-protected/pull/13.

Tagged:

Issue · Github
by Sheila

Issue Number
1044
State
closed
Last Updated
Closed By
vdauwera

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