The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

# Depth Reporting in DP and AD changes when VariantAnnotator run

Member Posts: 9

Hello,

I am trying to filter some of my high-coverage samples based on a minimum depth and have found that the value stored in the DP INFO field and the AD genotype tag changes depending on whether or not I have run VariantAnnotator. The call I have used for VariantAnnotator is:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R ucsc.hg19.fasta -I example.bam --variant example.raw.vcf --out example.annotated.vcf -G StandardAnnotation -L example.raw.vcf -rf BadCigar -dcov 15000

Here are the differences for some test cases with HaplotypeCaller:

No MarkDuplicates, did IndelRealigner & BQSR, nightly build 12/04/2013

Annotated: DP=2745, AD=4,2729

Raw: DP=957, AD=1,907

MarkDuplicates, IndelRealigner and BQSR, nightly build 12/04/2013

Annotated: DP=20, AD=0,20

Raw: DP=10, AD=0,8

Raw BAM, nightly build 12/04/2013

Annotated: DP=2745,AD=4,2729

Raw: DP=868, AD=1,864

Raw BAM, version 2.4-9

Annotated: DP=2745, AD=4,2729

Raw: DP=616, AD=1,611

I suspect what is happening here is that VariantAnnotator is taking the depth information from the provided BAM and replacing the depth information reported by the variant caller. Anyway, just wondering- which value is a better reflection of the depth used to make a given variant call? (i.e. which could I use in hard filtering?)

Thanks for your help!

Tagged:

## Answers

• Member Posts: 9

Great, thank you for confirming! In this case, I suspect we are seeing more genuine duplication (because of small, targeted areas and high coverage) than PCR duplication, so I'll have to do more testing to determine whether I should run MarkDuplicates.

• Administrator, Dev Posts: 11,124 admin

That's a fair point, if you know the duplicates are legit. From those values it looks like the results are consistent either way.

Geraldine Van der Auwera, PhD

Sign In or Register to comment.