How to filter out duplicate records in a vcf with bcftools?
Is there a bcftools command to remove duplicate records in a vcf file?
If a variant has duplicate records, I'd like to remove all entries of such variant in the vcf.
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Brice Sarver
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vitor.aguiar •
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vitor.aguiar •
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Exactly duplicated records?
If the records are truly identical, sort the file and use uniq.
Make sure the vcf isn't compressed before you pass or pipe!
Edit: I should clarify that you don't need to use BCFtools for this. So, use good-old regular uniq not bcftools uniq; that doesn't exist.
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beside unique can you take a look at this "Variant Normalization"
http://genome.sph.umich.edu/wiki/Variant_Normalization
http://blog.goldenhelix.com/grudy/variant-normalization-underappreciated-critical-infrastructure/
http://genome.sph.umich.edu/wiki/Vt
https://github.com/vcflib/vcflib#vcfuniq