Question: How to filter out duplicate records in a vcf with bcftools?
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vitor.aguiar • 10 wrote:
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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modified 4.4 years ago
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Brice Sarver • 3.6k
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4.4 years ago by
vitor.aguiar • 10
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