Question: BCFTools Query: Avoid grouping Alt Alleles
0
gravatar for jon.klonowski
13 months ago by
jon.klonowski70 wrote:

I am trying to query my vcf but I am running into a problem, the output looks like this:

chr17 61615660 chr17:61615660:T:TG,TC T TG,TC

where the columns are

Chr Pos ID REF ALT

and the line of code is:

bcftools query File_Name.vcf.gz -f'%CHROM\t %POS\t %ID\t %REF\t %ALT\n' -i'GT="alt"' | bgzip >  output.txt.gz

Is there a way to tell bcftools query not to group the alt alleles?

Thank you in advance.

ADD COMMENTlink written 13 months ago by jon.klonowski70

I imagine iteratting over each sample would solve this

bcftools query File_Name.vcf.gz -f'%CHROM\t %POS\t %ID\t %REF\t [%ALT]\n' | bgzip >  output.txt.gz

wrong

ADD REPLYlink modified 13 months ago • written 13 months ago by jon.klonowski70
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