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Progres meter Variant calling

Muriel_GBMuriel_GB Univ. Fribourg, SwitzerlandMember
edited November 2013 in Ask the GATK team


One can observe a progress meter when doing variant calling using HaplotypeCaller.

INFO  11:53:27,477 ProgressMeter - KE332547.1:3346983        8.24e+06   57.5 m        7.0 m      2.4%        39.4 h    38.4 h 

What are the different columns ?
Especially, what is the 1:3346983 ?

Thanks a lot !


Post edited by Geraldine_VdAuwera on

Best Answer


  • aminziaaminzia aminziaMember

    I am running UG on an exome target and see that ProgressMaster reports regions outside the capture intervals. Is the program reporting on regular intervals irrespective of the regions it actually processes or this is a bug in the UG (looking outside the target intervals). I am using GATK-3-1.1 and running the UG on targeted intervals give me Error Code 200.

    Thank you

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    Hi Amin,

    Can you please post your command line and the part of the progress meter showing the region you are interested in?

    What are the intervals it should be running on?


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