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.
• 7,399 views
•
link
updated
by
Brice Sarver
•
written
by
vitor.aguiar •
•
written
by
vitor.aguiar •
1 answer
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.
• 1 views
•
link
written
by
Brice Sarver
Log in to answer this question.
More posts like this
-
How does bcftools decide what sample name to assign when calling variants?
written by Paul •
-
Combine VCF files
written by Sowmya Pulapet •
-
how to remove positions in VCF based on rsID
written by raalsuwaidi •
-
How to set variant FILTER in a VCF file based on overlap with regions in a BED file
written by William
-
bcftools isec not producing sites.txt
written by steve
-
how to remove duplicate SNP rows in vcf using bcftools norm
written by evelyn
-
Removing both duplicates from a VCF
written by john.michel.rouhana •
-
vcf filter of lowQual
written by genomics Newbie •
-
Remove duplicate SNPs only based on SNP ID in bcftools
written by janhuang.cn
-
VCF to BCF file conversion
written by SOHAIL
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