Hi,
First, I want to know why when the AD of my data is 0,18 ,it converts the Genotypes from 1/1 to 0/1? (for example: GT:AB:AD:DP:GQ:PL:PP 0/1:.:0,18:20:5:309,21,0:265,0,5. The site number in vcf file is GWV0001275 ).
Second, the value of GQ decreased from 21 to 5 can be trusted?
Command Line-
java -Xms1g -Xmx30g -jar /home/zgong/GATK-3.7/GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R /bioinfo/data/Sequence/WholeGenomeFasta/genome.fa -V /data/gatk-anno.vcf.gz -o gatk.post.vcf.gz
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Some questions about the results of CalculateGenotypePosteriors
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