The current GATK version is 3.8-0
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!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Depth Reporting in DP and AD changes when VariantAnnotator run

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!

Best Answer

Answers

  • 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.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

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

Sign In or Register to comment.