Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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 f.name.bam --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 f.name.out

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

Best Answer

Answers

Sign In or Register to comment.