Attention:
The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

[possible-bug] GATK 3.4-46 CombineGVCFs is wrongly assigning * at -1 position of some intervals

We found that whenever the previous interval ends in a deletion, GATK is extending upstream 1 base the following interval and wrongly adds the * call to it. In most cases this will be a non-issue as you will filter downstream analysis with the same interval files and these lines won't be included. Still it looks like a bug the team might want to look into.

Also we are running CombineGVCFs in "BP_RESOLUTION" mode. Not sure if this makes a difference.

A couple of examples:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   100330153   .   C   <NON_REF>   .   .   .
1   100330154   .   T   <NON_REF>   .   .   .
1   100330155   .   TC  T,<NON_REF> .   .   BaseQRankSum=-0.572;ClippingRankSum=0;DP=14876;MQ=60;MQRankSum=-1.067;ReadPosRankSum=0.572
1   100335944   .   T   *,<NON_REF> .   .   DP=8
1   100335945   .   T   <NON_REF>   .   .   .
1   100335946   .   T   <NON_REF>   .   .   .

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   215916683   .   AAGAG   A,AAG   9405.15 .   AC=4,81;AF=0.008547,0.173;AN=468;BaseQRankSum=-0.061;ClippingRankSum=0.1;DP=25502;FS=0;InbreedingCoeff=-0.2174;MLEAC=2,80;MLEAF=0.004274,0.171;MQ=60;MQRankSum=0.092;QD=1.25;ReadPosRankSum=-1.035;SOR=0.65
1   215916684   .   A   *,<NON_REF> .   .   DP=25594
1   215916685   .   G   *,<NON_REF> .   .   DP=25593
1   215916686   .   A   *,<NON_REF> .   .   DP=25128
1   215916687   .   G   *,<NON_REF> .   .   DP=25115
1   215931925   .   T   *,<NON_REF> .   .   DP=65
1   215931926   .   T   <NON_REF>   .   .   .
1   215931927   .   T   <NON_REF>   .   .   .

Relevant lines in the interval file:

1   100329930   100330155   AGL 0   +
1   100335944   100336147   AGL 0   +
1   215916507   215916687   USH2A   0   -
1   215931925   215932104   USH2A   0   -

Thanks,
Carlos

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @CarlosBorroto
    Hi Carlos,

    I am not sure I follow what you are saying. Do you mean position 1:100335944 does not have a deletion in the GVCF, but in the Combined GVCF, it shows a deletion (*)? If so, then that is a bug and I will need you to submit some test files.

    Thanks,
    Sheila

  • CarlosBorrotoCarlosBorroto Member ✭✭

    Hi @Sheila,

    Yes, in the samples above positions 1:100335944 and 1: 215931925 are called as deletion but I don't think they are. I will collect test files and upload them to the FTP.

    --Carlos

Sign In or Register to comment.