Usage: bcftools +tag2tag [General Options] -- [Plugin Options]
Options:
   run "bcftools plugin" for a list of common options

Plugin options:
       --ORI-to-NEW           Convert from source tags FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT
       --QR-QA-to-QS          Convert FORMAT/QR,QA to FORMAT/QS
       --XX-to-LXX            Convert from normal to localized tags (from PL,AD to LAA,LPL,LAD)
       --LXX-to-XX            Convert from localized to normal tags (from LAA,LPL,LAD to PL,AD)
   -d, --defaults LIST        Values to use in place of missing --LXX-to-XX fields [AD:.,PL:.]
   -s, --skip-nalt INT        Do not modify sites with fewer (--XX-to-LXX) or more (--LXX-to-XX)
                              than INT alternate alleles, 0=all sites [0]
   -r, --replace              Drop the source tag
   -t, --threshold FLOAT      Threshold for GP to GT hard-call [0.1]

Examples:
   bcftools +tag2tag in.vcf -- -r --GP-to-GL
   bcftools +tag2tag in.vcf --    --PL-to-GT

   # Expand the family of localized tags (LPL,LAD,LAF) to normal tags (PL,AD,AF). With the -s 3
   # option, only sites with fewer than three alternate alleles will be expanded.
   # Note that FORMAT/LAA must be present.
   bcftools +tag2tag in.vcf -- --LXX-to-XX -s 3

   # The same as above, but convert only the LAD tag
   bcftools +tag2tag in.vcf -- --LAD-to-AD -s 3

   # Replace the family of normal tags (PL,AD,AF) with localized tags (LPL,LAD,LAF). With the -s 3
   # option, only sites with more than three alternate alleles will be modified. Note that in order
   # to remove the original tags, -r must be given.
   bcftools +tag2tag in.vcf -- --XX-to-LXX -s 3 -r

   # The same as above, but convert only the PL tag
   bcftools +tag2tag in.vcf -- --PL-to-LPL -s 3