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Question: How to filter out duplicate records in a vcf with bcftools?
0
gravatar for vitor.aguiar
4.4 years ago by
vitor.aguiar • 10
Brazil
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.
bcftools vcf • 4.9k views
ADD COMMENT • link •
modified 4.4 years ago by Brice Sarver • 3.6k • written 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

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by Medhat ♦ 8.8k

https://github.com/vcflib/vcflib#vcfuniq

ADD REPLY • link written 3.5 years ago by cpad0112 ♦ 14k
0
gravatar for Brice Sarver
4.4 years ago by
Brice Sarver • 3.6k
United States
Brice Sarver • 3.6k wrote:

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.
ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by Brice Sarver • 3.6k
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