Depth of coverage differing between DepthOfCoverage and HaplotypeCaller

mouradovmouradov AustraliaMember
edited September 2015 in Ask the GATK team

Hi, I am getting something peculiar.

I have a potential snv detected via HaplotypeCaller, with the allelic depth (AD) being given as 714,174. When I view this on IGV I get 714,4 as the depths, when I run DepthOfCoverage I also get 718 total reads at that position.

GATK version is 3.4.0

HaplotypeCaller -R ucsc.hg19.fasta -I --genotyping_mode DISCOVERY --dbsnp dbsnp_138.hg19.vcf -L regions.bed -stand_emit_conf 10 -stand_call_conf 30 --min_base_quality_score 20 -o

Full GRT GT:AD:DP:GQ:PL 0/1:714,174:888:99:3077,0,15131

Any ideas on the discrepancy. Thanks in advance.

Post edited by mouradov on

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