Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Same mutation from different samples are differently annotated in dbsnp database

zhaozhengzhaozheng beijing, chinaMember

Hello,

I try to call mutations for several samples by using mutect2. For some samples (such as WES443), a mutation of interest (chr2:201113112 based on hg19) is successfully annotated in dbSNP database - rs121913500. But, the mutation in a sample (WES449) is not successfully annotated in dbSNP database.
WES443
chr2 209113112 rs121913500 C T . PASS DB;ECNT=1;HCNT=24;MAX_ED=.;MIN_ED=.;TLOD=136.60 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:82,47:0.357:18:29:0.617:3162,1787:39:43

WES449
chr2 209113112 . C T . PASS ECNT=1;HCNT=8;MAX_ED=.;MIN_ED=.;TLOD=200.35 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:59,61:0.531:36:25:0.410:2339,2447:31:28

I'm not sure what the problem is? Could someone please give me some suggestion?

Thanks,

Zheng Zhao

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @zhaozheng
    Hi Zheng,

    Can you tell us the exact command you ran for each sample? Did you include the dbSNP file for each sample?

    Thanks,
    Sheila

  • zhaozhengzhaozheng beijing, chinaMember
    edited June 2017

    Hi Sheila,

    Very pleased to hear from you.

    The exact command I use is described below:

    open(R, "sample1.txt");
    while(){
    chomp;
    print "run sample $_\n";
    java -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T MuTect2 -R Homo_sapiens_assembly19_chr.fasta -I:tumor Bam/${_}.final.bam --dbsnp GenomeAnalysisTK-3.7/dbsnp_132_b37.leftAligned_chr.vcf --cosmic GenomeAnalysisTK-3.7/b37_cosmic_v54_120711_chr.vcf -L intervals.intervals -o Mutect2/${_}.output.vcf;
    }

    close R;

    The sample1.txt file contains all sample ids. The intervals.intervals file lists some region of interest like this:
    chr2:209100951-209101893
    chr2:209103795-209103957
    chr2:209104587-209105039
    chr2:209106718-209106869
    chr2:209108151-209108328
    chr2:209110043-209110148
    chr2:209112106-209113384
    chr2:209115985-209116291
    chr2:209118610-209119063
    chr2:209118755-209119046

    I hope I can get help from you.
    Best wishes.

    Zheng Zhao

  • SheilaSheila Broad InstituteMember, Broadie admin

    @zhaozheng
    Hi Zheng,

    Hmm. Okay, can you please run the command on both samples again on just that interval (chr2:209112106-209113384) ? Let us know if that exact command gives different results with respect to rsID.

    Thanks,
    Sheila

Sign In or Register to comment.