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.