GQ not included in bcf output - beginner question

[sagedale]

Hi bcftools team,

I am relatively new to bcftools and have a fairly beginner question. I called variants which produced PL in the format field, and then used the next code to try add GT and GQ to the format fields. The bcftools call added GT however didn't add GQ to the format field. I have updated bcftools from 1.14 to 2.22 in between these steps and am wondering if this is causing issues? I would like to filter for GQ downstream, but don't understand how to include it in my format field of my bcf? Thanks for your help!

1. Variant Calling (v. 1.14):

bcftools mpileup -E -O b
-f /bsuhome/sagedale/scratch/Peregrine/Genomes/Trimmed_Reads/Combined/GCF_023634155.1_bFalPer1.pri_genomic_SEQUENTIAL.fna
-a AD,ADF,DP,ADR,SP
-o /bsuhome/sagedale/scratch/Peregrine/Genomes/Trimmed_Reads/Combined/BAM/Sorted_BAM/BCFs/PEFA_Subsp_Indexed.bcf
/bsuhome/sagedale/scratch/Peregrine/Genomes/Trimmed_Reads/Combined/BAM/Sorted_BAM/*_sorted.bam

bcftools index /bsuhome/sagedale/scratch/Peregrine/Genomes/Trimmed_Reads/Combined/BAM/Sorted_BAM/BCFs/PEFA_Subsp_Indexed.bcf

2. Add GT and GQ (v. 1.22):

bcftools call -mv
-Ob -o PEFA_111725.bcf
PEFA_Subsp_Indexed.bcf