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, Moderator

    @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, Moderator

    @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

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