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.

Meaning of terms in output of GenotypeConcordance

blueskypyblueskypy Member Posts: 266 ✭✭
edited October 2013 in Ask the GATK team

Just to make sure my understanding is correct:

HET: heterozygous
HOM_REF: homozygous reference
HOM_VAR: homozygous variant
MIXED: something like `./1`
Mismatching_Alleles: ??
UNAVAILABLE: for internal use
ALLELES_MATCH: ??
ALLELES_DO_NOT_MATCH: ??
EVAL_ONLY: ??
TRUTH_ONLY: does it actually mean the variants present in comp but not in eval, like COMP_ONLY?

how does the following computed?

Non-Reference_Discrepancy
Non-Reference_Sensitivity  
Overall_Genotype_Concordance

Thanks a lot!

Answers

  • blueskypyblueskypy Member Posts: 266 ✭✭

    Could anyone please help with this? I appreciate!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,647 admin

    @blueskypy, I've asked the tool's author to answer you but he is very busy so you'll need to be a little patient.

    Geraldine Van der Auwera, PhD

  • chartlchartl 7ccMember Posts: 11 mod

    Hi blueskypy,

    Thanks for your patience. Your intuition on all counts has been correct.

    ALLELES_MATCH are counts of calls at the same site where the alleles match

    ALLELES_DO_NOT_MATCH are counts of calls at the same location with different alleles, such as the eval set calling a 'G' alternate allele, and the comp set calling a 'T' alternate allele.

    Eval only are the counts of sites present only in the eval VCF, and not in the comp.

    Non-reference sensitivity is the sensitivity of the eval calls to polymorphic calls in the comp set, that is (# true positive)/(# true polymorphic).

    Overall genotype concordance is just (# concordant genotypes)/(# genotypes)

    This tends to be high just because reference calls predominate; so we use in addition the Non-reference discrepancy, which, loosely, is the genotype concordance excluding concordant reference sites. See attached.

    pdf
    pdf
    nrd.pdf
    101K
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,647 admin

    For future reference, I'm adding this information to the GenotypeConcordance tool documentation, which will be updated with the next release.

    Geraldine Van der Auwera, PhD

  • blueskypyblueskypy Member Posts: 266 ✭✭

    Thanks, Geraldine! Happy New Year!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,647 admin

    Happy New Year to you too, and many successful GATK runs :)

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.