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 2.9.4 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.

EMIT_ALL_CONFIDENT_SITES for bacteria

ProtaeusProtaeus Member
edited October 2012 in Ask the GATK team

Hello,
I am running the variant caller to identify SNPs and Reference Calls in a bacterial genome, which means I am running with -ploidy 1, -glm POOLSNP and -prnm POOL as suggested in other regions of this forum. The tool does an excellent job when just looking for Variants, but when I attempt to EMIT_ALL_CONFIDENT_SITES, it just spits out the SNPs and not the reference calls. When I remove the arguments stating that it is ploidy of 1, it works fine but calls SNPs that shouldn't be there since it's assuming diploid. Thus, I would really like to be able to emit all sites in ploidy=1 mode. Any reason why this is not possible?
Thanks for you help!
John

Post edited by Geraldine_VdAuwera on

Best Answer

  • delangeldelangel Broad InstituteMember
    Accepted Answer

    Hi - yes, we also just noticed that emitting confident reference sites is broken when ploidy != 2. This should be fixed in the next couple of days, I'll let you know when this is ready.
    Note that when you update to the newer version (2.1.x) you'll have to change your command line back to -glm SNP, the POOL* arguments have been deprecated.

Answers

  • delangeldelangel Broad InstituteMember
    Accepted Answer

    Hi - yes, we also just noticed that emitting confident reference sites is broken when ploidy != 2. This should be fixed in the next couple of days, I'll let you know when this is ready.
    Note that when you update to the newer version (2.1.x) you'll have to change your command line back to -glm SNP, the POOL* arguments have been deprecated.

  • Thanks for the info and working to address the issue.
    Cheers,
    John

  • I noticed the same thing earlier on v2.1-8. I always run the UnifiedGenotyper with the EMIT_ALL_SITES option. But I've found that if I specify ploidy=1, every position where the genotype is same-as-reference is marked with LowQual. In many cases, the QUAL is NaN, in other cases it's just an extremely low number (<10). But the QUALs for SNPs look normal. Interestingly, when I run the same data with ploidy=2, everything looks great (normal/high QUALs for both SNPs and same-as-ref positions).

    I'll keep an eye out for 2.1-9.

  • delangeldelangel Broad InstituteMember

    Yes, we are aware of these issues when ploidy !=2. We are working on fixing the problem but may or may not be ready for 2.1-9, we will post here when the fix is out.

  • Has there been any progress on this front? The Sep 6th response on this thread sounded like it would be somewhat straightforward to fix the calculation of QUAL for same-as-ref sites for ploidy != 2.

  • delangeldelangel Broad InstituteMember

    It turned out that fix wasn't straightforward - it's been fixed but it will make it when we release 2.2, no ETA yet

  • I hate to dwell, but if I am reading the updates to2.2 correctly, this bug has not yet been addressed? Eta?

  • ebanksebanks Broad InstituteMember, Broadie, Dev

    It is in 2.2 as Guillermo said.

Sign In or Register to comment.