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.

Rank Sum Tests

volaviivolavii Member Posts: 17

Hey guys,

im struggeling with some statistics given by the vcf file: the Ranksumtests. I started googleing arround, but that turned out to be not helpfult for understanding it (in may case). I really have no idea how to interprete the vcf-statistic-values comming from ranksumtest. I have no clue whether a negative, positive or value near zero is good/bad. Therefore im asking for some help here. Maybe someone knows a good tutorial-page or can give me a hint to better understand the values of MQRankSum, ReadPosRankSum and BaseQRankSum. I have the same problem with the FisherStrand statistics. Many, many thanks in advance.

Best Answer

  • pdexheimerpdexheimer Member, Dev Posts: 544 ✭✭✭✭
    Accepted Answer

    The rank sum metrics use the Wilcoxon Rank Sum test, which tests whether or not two populations are the same (from the same distribution). The actual metric is the Z-score of the test, not the direct U score - see the "Normal approximation" section on the wiki page. The major takeaway is that values close to zero are "good" (less difference between reads containing the reference and alternate reads), while higher magnitude values reflect larger differences

Answers

  • pdexheimerpdexheimer Member, Dev Posts: 544 ✭✭✭✭
    Accepted Answer

    The rank sum metrics use the Wilcoxon Rank Sum test, which tests whether or not two populations are the same (from the same distribution). The actual metric is the Z-score of the test, not the direct U score - see the "Normal approximation" section on the wiki page. The major takeaway is that values close to zero are "good" (less difference between reads containing the reference and alternate reads), while higher magnitude values reflect larger differences

Sign In or Register to comment.