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GATK calling on del/ins at same location

sgoyalsgoyal San CarlosMember

Hi there,

I mapped using both BWA and novoalign.
In my sample on gene DHCR7 on chr11, there is Deletion and Insertion at same location. Del of 4 bases (GACG) at chr11: 71,155,132 - 71,155,135 AND insertion of 11 bp CGTCACCGGAC

After alignment in IGV, it shows up as insertion of CGTCACCG between 71,155,131 and 71,155,132 and deletion of bp 71,155,135 (G) . It ends up being called as separate variant which is wrong

IGV is attached. Any inputs of correcting is appreciated. How does GATK algorithm handles this - how about local realignment by haplotyper ?

Swati

Best Answer

Answers

  • sgoyalsgoyal San CarlosMember

    Adding 2 lines from vcf that display the variant in wrong form

    11 71155131 . T TCGTCACCG 48105.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=12.360;ClippingRankSum=-0.967;DP=2475;ExcessHet=3.0103;FS=4.127;MLEAC=1;MLEAF=0.500;MQ=69.81;MQRankSum=-1.408;QD=19.47;ReadPosRankSum=-10.501;SOR=1.009 GT:AD:DP:GQ:PL 0/1:1263,1208:2471:99:48143,0,49127
    11 71155134 . CG C 47072.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=23.885;ClippingRankSum=-1.123;DP=2446;ExcessHet=3.0103;FS=3.285;MLEAC=1;MLEAF=0.500;MQ=69.81;MQRankSum=-1.846;QD=19.24;ReadPosRankSum=-10.971;SOR=0.947 GT:AD:DP:GQ:PL 0/1:1238,1208:2446:99:47110,0,49231

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @sgoyal
    Hi Swati,

    Can you post the bamout file?

    Thanks,
    Sheila

  • sgoyalsgoyal San CarlosMember

    Sure. However attached are zipped files, here is the command i used

    java -jar $GATK -T HaplotypeCaller -R hg19.fasta -I B2016_71154132_71156132.bam -o varaints.vcf -L 11 -bamout B2016_bamout.bam

  • sgoyalsgoyal San CarlosMember

    hmm.. seems like i am unable to upload files here. I am putting them on ftp , the file name is swati_nov21.tar.gz

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @sgoyal
    Hi Swati,

    I just needed the IGV screenshot. I received the file, no need to put onto the FTP.

    -Sheila

  • sgoyalsgoyal San CarlosMember

    Sure. top one is bamout.bam, the one below is original bam

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @sgoyal
    Hi Swati,

    How do you know the deletion and insertion exist at the same location? From the IGV screenshots, it looks like HaplotypeCaller is doing the right thing.

    -Sheila

  • sgoyalsgoyal San CarlosMember

    We confirmed it on sanger. They are not individual variants, its known pathogenic frame shift mutation of 4 bp deletion and 11 bp insertion.

    Issue · Github
    by Sheila

    Issue Number
    1467
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @sgoyal
    Hi Swati,

    Can you post the original BAM file that was not pre-processed? Does it show the insertion and deletion at the same location?

    -Sheila

  • sgoyalsgoyal San CarlosMember

    Yes, it shows at same location. Processing didnt change anything on those reads.

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