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!

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.

Did you remember to?


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
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Low QD Value for Well-Supported High-Coverage SNPs- other annotations to use?

nhvanlienhvanlie Member Posts: 9

Hello,

I am hoping to perform hard filtering on some variants from a sequencing project where, unfortunately, I do not have information from enough samples for VQSR. I was planning to filter on the QD value, but it seems to be very low for variants that seem reasonable. Example:

chr7    55249063 .       G       A       225     PASS
AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=1.307;DP=4582;DP4=937,935,1299,1316;Dels=0.00;FQ=225;FS=0.323;
HaplotypeScore=390.2899;MQ=59.95;MQ0=0;MQRankSum=-1.910;PV4=0.81,1,1,1;QD=0.05;ReadPosRankSum=4.848;VDB=0.0003
GT:AD:GQ:PL     0/1:1917,2657:99:255,0,255

This variant is shown in IGV in the attached file- it looks to be a true positive, but because of the high depth, QD is very low. Based on the QD documentation, it looks as QD simply cannot be used to filter high-coverage data, since the value is QUAL/unfiltered depth.

Is there an alternative annotation that expresses the same measure, since QD is recommended in all the hard filtering documentation? Would GQ be a good substitute?

Your help is much appreciated!

IGV_QD_mysterious.png
1061 x 688 - 25K

Best Answer

Answers

  • nhvanlienhvanlie Member Posts: 9

    Correct- these calls are produced with samtools mpileup. I will try to determine a better cutoff for this data. Thanks for your help!

Sign In or Register to comment.