No PTAprob values in *.snvs.ptato.vcf.gz

[moshl]

Hi Mark,

The output of the demo data looks good!
I‘m running scWES data produced by ResolveOME kit. The input VCF has chromosome names with the chr prefix, and I’ve also modified some of your R scripts for PTATO. However，I’m seeing that PTAprob values are missing from the output *.snvs.ptato.vcf.gz. Why might this be happening, and how can I fix it?

I appreciate any guidance.

Best regards,
Mo

zcat EB357.HC.snp_indel.filter_EB357.snvs.ptato.vcf.gz |grep -v "#" |head -2

chr1 1287557 chr1:1287557_G/A G A 115.91 PASS ABSENT_CONTROLS=1;ABSENT_CONTROL_NAMES=B145P3CD45;ABSENT_SAMPLES=0;ABSENT_SAMPLE_NAMES=.;AC=1;AF=0.25;AN=4;BaseQRankSum=1.52;CLONAL_CONTROLS=0;CLONAL_CONTROL_NAMES=.;CLONAL_SAMPLES=1;CLONAL_SAMPLE_NAMES=EB357;DP=51;ExcessHet=3.0103;FAIL_QC_CONTROLS=0;FAIL_QC_CONTROL_NAMES=.;FAIL_QC_SAMPLES=0;FAIL_QC_SAMPLE_NAMES=.;FS=8.751;MLEAC=1;MLEAF=0.25;MQ=60;MQRankSum=0;PASS_QC_CONTROLS=1;PASS_QC_CONTROL_NAMES=B145P3CD45;PASS_QC_SAMPLES=1;PASS_QC_SAMPLE_NAMES=EB357;QD=11.59;ReadPosRankSum=0.712;SOR=0.02;SUBCLONAL_CONTROLS=0;SUBCLONAL_CONTROL_NAMES=.;SUBCLONAL_SAMPLES=0;SUBCLONAL_SAMPLE_NAMES=. GT:AD:CAD:DP:FT:GQ:PGT:PID:PL:SB:VAF 0/1:6,4:7,4:10:PASS:99:.:.:124,0,140:.,0,0,0:0.36
chr1 1657260 chr1:1657260_G/A G A 1044.91 PASS ABSENT_CONTROLS=1;ABSENT_CONTROL_NAMES=B145P3CD45;ABSENT_SAMPLES=0;ABSENT_SAMPLE_NAMES=.;AC=1;AF=0.25;AN=4;BaseQRankSum=4.6;CLONAL_CONTROLS=0;CLONAL_CONTROL_NAMES=.;CLONAL_SAMPLES=1;CLONAL_SAMPLE_NAMES=EB357;DP=135;ExcessHet=3.0103;FAIL_QC_CONTROLS=0;FAIL_QC_CONTROL_NAMES=.;FAIL_QC_SAMPLES=0;FAIL_QC_SAMPLE_NAMES=.;FS=0;MLEAC=1;MLEAF=0.25;MQ=58.45;MQRankSum=0.204;PASS_QC_CONTROLS=1;PASS_QC_CONTROL_NAMES=B145P3CD45;PASS_QC_SAMPLES=1;PASS_QC_SAMPLE_NAMES=EB357;QD=10.66;ReadPosRankSum=0.21;SOR=0.66;SUBCLONAL_CONTROLS=0;SUBCLONAL_CONTROL_NAMES=.;SUBCLONAL_SAMPLES=0;SUBCLONAL_SAMPLE_NAMES=. GT:AD:CAD:DP:FT:GQ:PGT:PID:PL:SB:VAF 0/1:62,36:75,41:99:PASS:99:.:.:1053,0,1866:.,0,0,0:0.35