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.

positive and negative set in model training by variantRecalibrator

Hello!

Thanks for develop this tool set and share with others with good supports, it really contains a lot of wonderful tools.

I just try to understand VQSR more into detail. If I give the resources (dbsnp, hap map and 1kg omni data) recommended by the best practice with default settings (which one is in training, which one is the true set ...), Does the positive set contain all variants which recorded in the resources having train=TRUE, but how does the tool select negative set? Does it order the variants from high to low by the QUAL value, and pick up the 5% from the bottom (if the percentBad = 0.05)? Will there be some overlap between positive set and negative set? And is there any quality filtration on the data, e.g. one date point is more than a standard deviation away from average...

Thanks

Best Answer

Answers

  • ying_sheng_1ying_sheng_1 Posts: 74

    Thanks Geraldine. I think you answer all my questions.

Sign In or Register to comment.