Expanding gVCF box from GATK
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16 months ago
Axzd ▴ 80

Hello,

I wanted to expand the gVCF block of my vcf but I got this as a result

##bcftools_convertCommand=convert --gvcf2vcf -f Adineta_vaga.fsa; Date=Tue Aug  1 11:51:21 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ancestor
Chrom_3 793     .       G       T       172.33  .       AC=2;AF=1;AN=2;DP=10;ExcessHet=3.0103;FS=0;InbreedingCoeff=0.4054;MLEAC=3;MLEAF=0.5;MQ=25;QD=21.54;SOR=4.407    GT:AD:DP:GQ:PL  1/1:0,3:3:9:89,9,0
Chrom_3 1387    .       A       T       66.18   .       AC=0;AF=1;AN=0;DP=2;ExcessHet=3.0103;FS=0;InbreedingCoeff=0.354;MLEAC=1;MLEAF=0.5;MQ=27;QD=33.09;SOR=2.303      GT:AD:DP:GQ:PGT:PID:PL:PS       ./.:0,0:0:.:.:.:0,0,0:.
Chrom_3 1398    .       C       T       66.18   .       AC=0;AF=1;AN=0;DP=3;ExcessHet=3.0103;FS=0;InbreedingCoeff=0.354;MLEAC=1;MLEAF=0.5;MQ=27;QD=33.09;SOR=2.303      GT:AD:DP:GQ:PGT:PID:PL:PS       ./.:

That doesn't seem so expanded to me ^^' Any idea what might have gone wrong? The command I used is in the code above/

GATK VCF gVCF • 481 views
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