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Today seems the day of many questions Could I just add one more question : I am using VariantsToTable function , and although some fields in the VCF files contain all the data : eg
chr21 5148899 . C A . PASS ECNT=1;FS=0.000;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=8.71;TLOD=29.85 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:36,16:0.308:9:7:0.438:816,374:11:25 0/0:29,0:0.00:0:0:.:702,0:13:16
in the output TABLE file it is shown as :
chr21 5148899 . C A -10.0 NA NA
Why the AD and AF fields appear as NA ? thanks !
the command I am using is :
$GATK -T VariantsToTable \
-R $REFERENCE_HG38 \
-V file.analysis-MUTECT2.vcf \
-F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F AD -F AF \
-o output.TABLE.txt \