Calculating Allele Balance in GATK4

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!

gatk

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updated 4.8 years ago by astrinaki_maria •

• written 5.5 years ago by MAPK

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

Thanks a lot, Maria

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written 4.8 years ago by astrinaki_maria •

0 answers

No answers yet.

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