Hello,
I want to filter a vcf file by eliminating all the SNPs which have INFO <= 0.4.
In the shell, I therefore enter the following command : bcftools filter -e 'INFO<=0.4' myfile.vcf.gz The command runs for a veeeeeeery long time and, at the end, the file remains exactly the same. I have the feeling that it just reads all my file but nothing is filtered.
How could I modify my command to get a real filtering ? Thanks for any help.
bcftools filter -e 'INFO/info<=0.4' myfile.vcf.gz
Question! After getting vcf files back from the Michigan server, I noticed I don't have an 'INFO/info' value. Checking within my headers, this command:
bcftools view --header-only input.vcf | grep "ID=INFO"
Doesn't produce anything. Would you know the reason why this happens/a way around it?
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what is the definition in the header of this 'INFO' field ?
I get this :
So, is it uppercase INFO or lowercase info ??
I have paste the response as I got it. But clearly it is uppercase because if I try to enter the command with 'info', I get : Error: the tag "info" is not defined in the VCF header.
Question! After getting vcf files back from the Michigan server, I noticed I don't have any 'ID=INFO' within my header (running your command above outputs nothing). Would you know the reason why this happens/a way around it?
Hi,
I am trying to filter all SVTYPE=BND variants and this is what i tried
I could do it through
grep -vbut I am seeing if I could use bcftoolsPlease do not add answers unless they actually do answer the question. Just in case, try surrounding your expression in quotes:
-i 'SVTYPE!="BND"'. Also, ifSVTYPEis anINFOfield, use-i 'INFO/SVTYPE!="BND"'.