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# UnifiedGenotyper

edited July 2012

A new tool has been released!

Check out the documentation at UnifiedGenotyper.

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• Posts: 6Member

Hi all, I'm testing the GATK tools version 2.0 on two sample test and when I run UnifiedGenotyper I got a genotype only for the first sample I tested two different pair of samples

Using the version 2.1, instead, I got randomly this errors: Unexpectedly couldn't find valid codec for temporary output file /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub2916516663872161881.tmp

Many thanks for any suggestion you could have

Vincenza

• Posts: 679GATK Developer mod

Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

• Posts: 3Member

The UnifiedGenotyper documentation lists "We only handle diploid genotypes" as a caveat, but non-diploid organisms have been supported since version 2.0, right?

Yes indeed, we'll update that doc. Thanks for pointing this out.

Geraldine Van der Auwera, PhD

• Posts: 13Member

Just out of curiousity, how does UnifiedGenotyper handle "Alternative hits" aligned by BWA. Sometimes BWA will provide a couple of "Alternative hits" labled as XA, attached after MD field. The "Alternative hits" have exactly the same CIGAR and Edit distance as the following read. But why the position is negative? If the mapping quality is 0, does that mean no matter where the read is placed the contribution to SNP sites are exactly the same?

Read1 99 chr3 102778202 23 74M = 102778235 107 TTCCATCCTTTACATCCTTCTGTCTGTTCAAGAACCAGTCTGGGATCTTGCACTGGCGTGGATTCTGCATAATG __eceeceee^ec[^faadfbfgb_geeg[ba[ZdeaZ^affXbafd_dghghbaegaYZWbdbSV\\BBBB RG:Z:b_T_s_6 XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:3 X1:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:50T21C1 XA:Z:chr6_cox_hap1,-4623896,74M,1;chr6,-33351737,74M,1;chr6_qbl_hap2,-4429945,74M,1;

Read2 145 chr3 32664948 0 74M chr12 23364897 0 TCTCTGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTGTCATGCCTCAGCCTCCTGAGTAGGTGAGATT ]]]^b^VZRXdc\eZ\Tdadce^aeada_fdggcc[eaZffagdddZhgfgfeadaebeZacc[_ RG:Z:b_T_s_6 XT:A:R NM:i:4 SM:i:0 AM:i:0 X0:i:11 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:4A37C2C20C7 XA:Z:chr7,+99663378,74M,4;chr19,-49748273,74M,4;chr6,+43390671,74M,4;chr6,-166619724,74M,4;chr16,-66013198,74M,4;chr6,-33378145,74M,4;chr6_cox_hap1,-4650316,74M,4;chr6_qbl_hap2,-4456363,74M,4;chr9,-90294789,74M,4;chr4,+111287474,74M,4;

The UG, like most if not all the GATK tools, will simply ignore alternative hits and any reads with mapping quality of zero.

Geraldine Van der Auwera, PhD

• Posts: 1Member

This is my fifth time visiting this site. I still can't find what I want. I just wanna call snps. I need a simple intuitive example. All useless link and stupid docs. Can't you think like a normal person to present your tutorial?