Calculating Allele Balance in GATK4

Question

[MAPK]

Hi All,

I know GATK3 has option to compute Allele Balance and populate ABHet and ABHom fields. I do not see this option in GATK4. I used to run this command in GATK3:

java ${JAVAOPTS} -jar /usr/local/genome/GATK-3.6-0/GenomeAnalysisTK.jar -T VariantAnnotator -A AlleleBalance -I AF1.vcf.gz -R ${REF} -o AF1-ABannottated2.vcf.gz

Can someone please help me with the option I have if I am using GATK4. Thanks in advance!

[astrinaki_maria]

Hi MAPK, I face the same problem. Did you find the answer ?

Thanks a lot, Maria