Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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 \