Calculating Allele Balance in GATK4
0
0
Entering edit mode
2.7 years ago
MAPK ★ 2.0k

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 • 923 views
ADD COMMENT
0
Entering edit mode

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

Thanks a lot, Maria

ADD REPLY

Login before adding your answer.

Traffic: 1128 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6