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A question about IndelRealigner run log.

jh8gatkjh8gatk Member Posts: 7
edited September 2012 in Ask the GATK team

After I ran "IndelRealigner" tool, I saw the following message in the end of the run log, is it normal that 0 reads were filtered out during this step?

-------
INFO  07:01:50,692 TraversalEngine - 0 reads were filtered out during traversal out of 1529770054 total (0.00%) 
-------

JH

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin
    Accepted Answer

    This shouldn't be a cause for alarm -- what it means is that all the reads in your dataset passed the internal quality filters. But if you have reason to believe some of the reads should fail to pass the filters, you can always perform quality control on your dataset. If there is a big discrepancy, then you can start worrying...

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin
    Accepted Answer

    This shouldn't be a cause for alarm -- what it means is that all the reads in your dataset passed the internal quality filters. But if you have reason to believe some of the reads should fail to pass the filters, you can always perform quality control on your dataset. If there is a big discrepancy, then you can start worrying...

    Geraldine Van der Auwera, PhD

  • sboylesboyle Bay Area, CAMember Posts: 28
    edited November 2012

    I have a similar answer from a run of the "IndelRealigner" tool:

    INFO 14:55:38,633 ProgressMeter - Total runtime 8605.80 secs, 143.43 min, 2.39 hours

    INFO 14:55:38,683 MicroScheduler - 0 reads were filtered out during traversal out of 186330809 total (0.00%)

    INFO 14:55:38,684 NSRuntimeProfile - Input time: 18.2 s ( 0.21%)

    INFO 14:55:38,684 NSRuntimeProfile - Map time: 119.8 m (83.85%)

    INFO 14:55:38,684 NSRuntimeProfile - Reduce time: 11.0 s ( 0.13%)

    INFO 14:55:38,684 NSRuntimeProfile - Outside time: 22.6 m (15.81%)

    However, when I ran the "RealignerTargetCreator" tool i received the following result:

    INFO 12:29:39,213 ProgressMeter - Total runtime 3112.21 secs, 51.87 min, 0.86 hours

    INFO 12:29:39,214 MicroScheduler - 25366604 reads were filtered out during traversal out of 185663684 total (13.66%)

    INFO 12:29:39,214 MicroScheduler - -> 1257109 reads (0.68% of total) failing BadMateFilter

    INFO 12:29:39,214 MicroScheduler - -> 22900187 reads (12.33% of total) failing DuplicateReadFilter

    INFO 12:29:39,214 MicroScheduler - -> 1209307 reads (0.65% of total) failing MappingQualityZeroFilter

    INFO 12:29:39,216 MicroScheduler - -> 1 reads (0.00% of total) failing UnmappedReadFilter

    INFO 12:29:39,216 NSRuntimeProfile - Input time: 3.5 h (69.36%)

    INFO 12:29:39,217 NSRuntimeProfile - Map time: 65.7 m (21.84%)

    INFO 12:29:39,217 NSRuntimeProfile - Reduce time: 3.5 m ( 1.18%)

    INFO 12:29:39,217 NSRuntimeProfile - Outside time: 22.9 m ( 7.62%)

    My specific questions are:

    1) Is it odd that the RealignerTargetCreator tool found so many reads that failed filter and the IndelRealigner did not?

    2) Is it problematic that the number of reads claimed by the programs (186330809 vs 185663684 - There are more reads claimed by the IndelRealigner) are different?

    Thank you for the help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Nothing to worry about; these tools simply use different read filters by default.

    Geraldine Van der Auwera, PhD

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