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BCFTools Query: Avoid grouping Alt Alleles
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20 months ago

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.

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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

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