8000 Order of samples in family SNV and SV VCFs is different · Issue #650 · nf-core/raredisease · GitHub
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Order of samples in family SNV and SV VCFs is different #650

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sitems opened this issue Nov 30, 2024 · 1 comment
Open

Order of samples in family SNV and SV VCFs is different #650

sitems opened this issue Nov 30, 2024 · 1 comment
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sitems commented Nov 30, 2024

I am doing trio analysis, and noticed that the order of sample names in call_sv/genome/${FAM}_sv.vcf.gz and call_snv/genome/${FAM}_snv.vcf.gz is different, what causes small problems in my downstream analyses. It would be great if the order was the same.
@jemten jemten added enhancement Improvement for existing functionality Effort low and removed enhancement Improvement for existing functionality labels Dec 2, 2024
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jemten commented Dec 2, 2024

Thanks for submitting the issue @sitems.
I agree that it would be preferable to have them in the same order and we'll try to fix this in an upcoming release. In the meantime you can reorder the sample columns of your vcf using bcftools view --samples sample1,sample2,sample3 input.vcf

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