Merge different vcf files
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11 months ago

Hi, I have some vcf files in which some ref alleles are different for the same region. Can I merge all vcf files or do I have to standardize these ref alleles?

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Normalize them first using vt normalize or bcftools norm - they need to be in left-aligned parsimonious representation before you can do an accurate merge if required.

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Thank you!

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