bcftools +tag2tag --GP-to-GT

[rcheng]

bcftools 1.23.1
"-t, --threshold FLOAT Threshold for GP to GT hard-call [0.1]"

However, smaller thresholds result in more missing genotypes (see the attached screenshot for examples; the input file is the same). Is this expected?

Interestingly "-t 1" imputes all missing genotypes as desired.

Em... found "ptr[jmax] < 1 - args->gp_th" in the code.

[pd3]

Thank you for the issue. The usage page seems to advertise the opposite of what the program is actually doing.

Also, the advertised default value did not match the implementation. This is now fixed.

For reference, the problem was introduced in the original commit here 206c4ee.