How to filter vcf files with bcftools and to check whether the filtering worked
Hi guys, I have to filter a vcf file removing REF allele being equal to N. I wrote the following command line:
bcftools view -e 'REF = "N"' HT_Third_10_Plates_Batch.vcf > HT_Third_10_Plates_Batch_withoutN.vcf
But I'm not sure it worked... I got a HT_Third_10_Plates_Batch_withoutN.vcf as big as the input, and I know there are REF allele being equal to N.
How can I be sure it worked? Is it the command correct?
Thank u!
• 984 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
Khaleesi95 •
•
written
by
Khaleesi95 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
The allele with index 2 is not defined in the REF/ALT columns" error after AF filtering with gnomAD…
written by erikatatianacs •
-
How to Resolve Reference Mismatch While Extracting Gene Variants from 1000 Genomes Project Phase 3 …
written by Rohan •
-
how to convert bcf files into bgen
written by Khaleesi95 •
-
How to remove the white background from my table
written by Khaleesi95 •
-
How to create a new VCF 1) filtered by samples, and 2) with only selected fields
written by ariel
-
Filtering out samples by FORMAT attributes using bcftools
written by scottbrainard •
-
Bcftools filter error
written by BAGeno
-
bcftools view filter exclude not working when using logical operators
written by curious
-
Extract columns from VCF file using bcftools preserving all the header info
written by nikitavlassenko
-
Script that converts VCF file to reference allele format?
written by dktldkrh13 •
Simplest way is by counting the lines.