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.

Update of AD field after SelectVariants

mbauermbauer Member Posts: 1
edited November 2012 in Ask the GATK team

Hi,

I used the UnifiedGenotyper (GATK 1.6) on a multi-sample set to call variants, and for some of the positions I get multiple mutated alleles. The genotype entries in the combined VCF file look like (GT:AD:DP:GQ:PL):

0/1:94,11,0:124:22.18:22,0,2485,209,2500,2709

0/2:27,0,54:81:99:1651,1726,2695,0,968,836

so it's three AD values per entry. Running SelectVariants yields the following line for the second example from above:

GT:AD:DP:GQ 0/1:27,0,54:81:99

Although it changed the genotype from 0/2 to 0/1, it did not update the AD field. I checked the forums, but I could not really find anything discussing specifically the update of AD, except for the GATK 2.2 release notes where it says SelectVariants: "Fixed bug where the AD field was not handled properly. We now strip the AD field out whenever the alleles change in the combined file."

I was wondering whether you could confirm if cases like the one above would benefit from the bugfix, or if the bug description applies to something else.

Thanks a lot for all your hard work,
Markus

Post edited by Geraldine_VdAuwera on

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 admin

    Correct, this is the fix that was reported.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • b0bb0b Member Posts: 1

    For a variant that has been stripped of the AD field, is there any way/tool avalibe that can re-populate this field? In the case of the AD field it is not clear to me why all values needed to be droped rather than just the value for the dropped allele. Cheers.

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 admin

    No, this isn't possible currently. One should theoretically be able to use the Variant Annotator, but it's not hooked up appropriately with this particular annotation at the moment (but we're hoping to fix this at some point).

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

Sign In or Register to comment.