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Reference Homozygous AD problem

Dear GATK team,

I am using GATK 4 and I found curious output in gVCF file.

my command was:

gatk --java-options "-Xmx8G -Djava.io.tmpdir=$PWD/tmp -XX:ParallelGCThreads=$cpu" HaplotypeCaller -R $hg38 -I ${arg%.bam}.recal.bam -ERC BP_RESOLUTION --max-alternate-alleles 1 -O ${arg%.bam}.raw.snps.g.vcf -L $bed --dbsnp $dbsnp

And one of the variants (I found many more) is:

chr17 30237328 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:23,19:42:0:0,0,154

I do not understand AD is 23,19 at this 0/0 site. I would expect result like AD=42,0 (for reference homozygous).

Can anybody explain me how is possible that allelic depth is split to two values if only one allele is appearing? Also in IGV I can see only T are in aligned reads at this site.





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