Filter records by presence/absence of GT field?

[rajwanir]

Hi @pd3

Is there a way to filter out records that do not have GT set altogether (not missing GT)? For example, remove a record like below with GT unset:

chr1 13853 cnvi0081369 C . . PASS GC=0.5675;ALLELE_A=-1;ALLELE_B=-1;FRAC_A=0.254902;FRAC_C=0.166667;FRAC_G=0.343137;FRAC_T=0.235294;NORM_ID=0;BEADSET_ID=124;INTENSITY_ONLY;ASSAY_TYPE=0 BAF:LRR:NORMX:NORMY:R:THETA:X:Y 0:-0.493254:0.737172:0.0338293:0.771002:0.0291944:11958:1161

from a BCF that contains most records like below:

chr1 629731 MitoT4562C T C . PASS GC=0.425;ALLELE_A=0;ALLELE_B=1;FRAC_A=0.270492;FRAC_C=0.139344;FRAC_G=0.278689;FRAC_T=0.311475;NORM_ID=5;BEADSET_ID=56;ASSAY_TYPE=0;AC=0;AN=2 GT:GQ:IGC:BAF:LRR:NORMX:NORMY:R:THETA:X:Y 0/0:2:0.381889:0:-0.249051:3.92626:0.30878:4.23504:0.0499641:48920:6639

I think it would be query to simply check FORMAT/GT tag is present but couldn't write the correct expression. I came across an older issue where it seems like it may not be feasible with standard bcftools supported expressions (#1028).

Is this feasible?

Thank you.