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!

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!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
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.

Does setting the -out_mode flag in UnifiedGenotyper differently has different effect when doing VQSR

rkanwarrkanwar Member Posts: 2
edited October 2012 in Ask the GATK team

Hello,

Does VQSR behave differently when the -out_mode flag in UnifiedGenotyper is set to EMIT_VARIANTS_ONLY as compared to EMIT_ALL_CONFIDENT_SITES. I think by using EMIT_ALL_CONFIDENT_SITES we might give VQSR more information to train the model, but I may be wrong. Can someone please help me with this ? Thanks.

cheers,
Rahul

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin
    Accepted Answer

    Hi Rahul,

    Emit all confident sites produces confident reference calls too. But they are ignored by the default VQSR mode (SNPs only) so it shouldn't matter. But they aren't ignored if running in BOTH mode.

    In either case, it's definitely not recommended practice to train off of monomorphic sites as it defeats the purpose of the training.

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin
    Accepted Answer

    Hi Rahul,

    Emit all confident sites produces confident reference calls too. But they are ignored by the default VQSR mode (SNPs only) so it shouldn't matter. But they aren't ignored if running in BOTH mode.

    In either case, it's definitely not recommended practice to train off of monomorphic sites as it defeats the purpose of the training.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.