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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
Unable to parse header with error: /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub466622677294089813.tmp (Too many open files), for input source: /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub466622677294089813.tmp
Many thanks for any suggestion you could have
Please search around for answers before posting questions as you'll see that most questions have already been addressed already:
Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT
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
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^VZR`Xdc\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.
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?
I understand your frustration; this is a complex topic, and we are aware we need to improve our documentation. That is an ongoing effort, and we always appreciate constructive feedback.
However, this forum is not an appropriate channel for venting your frustration. This is a space for professionals to exchange information. Childish tantrums will not be tolerated.
Here's a simple and intuitive piece of advice: if you would like someone to help you (for free, I might add), don't be rude. Lose the attitude and you might get what you need.
If you don't like it, you're free to use a different software package.