Hi there, i'm trying to extract fields from VCF file using BCFTOOLS : The command :

bcftools query -f '%CHROM\t %POS\t %REF\t %ALT\t [%DP]\t [%AD]\t [%AF]\t [%MQ]\t [%GQ]\t %QUAL\t [%FS]\n' file.vcf > extract.tsv

I want to have output like this :

CHROM=1 POS=12783 REF=G ALT=A DP=19 AD=15
AF=0.5 MQ=26.6 GQ=87 QUAL=334.77 FS=0

Instead of this :

CHROM=1 POS=12783 REF=G ALT=A DP=19 AD=4,15
AF=0.5 MQ=26.6 GQ=87 QUAL=334.77 FS=0

I don't want to have the AD for reads that support the reference Can anyone help!

Or is there any command That can remove the Numbers before ',' in AD field. Thank youuu

EDIT : I just found the solution :

 bcftools query -f 'CHROM=%CHROM\t POS=%POS\t REF=%REF\t ALT=%ALT\t DP=[%DP]\t AD=[%AD**{1}**]\t AF=[%AF]\t MQ=[%MQ]\t GQ=[%GQ]\t QUAL=%QUAL\t FS=[%FS]\n' file.vcf > extract.tsv

[%AD{1}] : {1} will extract the second value and {0} The first.