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Local Realignment around Indels

delangeldelangel Posts: 71Dev mod
edited June 21 in Methods and Algorithms

For a discussion of the implications of removing indel realignment from workflows, see Blog#7847 from June 2016.

Realigner Target Creator

For a complete, detailed argument reference, refer to the GATK document page here.

Indel Realigner

For a complete, detailed argument reference, refer to the GATK document page here.

Running the Indel Realigner only at known sites

While we advocate for using the Indel Realigner over an aggregated bam using the full Smith-Waterman alignment algorithm, it will work for just a single lane of sequencing data when run in -knownsOnly mode. Novel sites obviously won't be cleaned up, but the majority of a single individual's short indels will already have been seen in dbSNP and/or 1000 Genomes. One would employ the known-only/lane-level realignment strategy in a large-scale project (e.g. 1000 Genomes) where computation time is severely constrained and limited. We modify the example arguments from above to reflect the command-lines necessary for known-only/lane-level cleaning.

The RealignerTargetCreator step would need to be done just once for a single set of indels; so as long as the set of known indels doesn't change, the output.intervals file from below would never need to be recalculated.

 java -Xmx1g -jar /path/to/GenomeAnalysisTK.jar \
  -T RealignerTargetCreator \
  -R /path/to/reference.fasta \
  -o /path/to/output.intervals \
  -known /path/to/indel_calls.vcf

The IndelRealigner step needs to be run on every bam file.

java -Xmx4g \
  -jar /path/to/GenomeAnalysisTK.jar \
  -I <lane-level.bam> \
  -R <ref.fasta> \
  -T IndelRealigner \
  -targetIntervals <intervalListFromStep1Above.intervals> \
  -o <realignedBam.bam> \
  -known /path/to/indel_calls.vcf
  --consensusDeterminationModel KNOWNS_ONLY \
  -LOD 0.4
Post edited by shlee on


  • medhatmedhat PolandPosts: 13Member
    edited May 25

    IT gives me this error : ##### ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@301da01d appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 65. Please see for more details and options related to this error. Any IDea?? "this link does not take me to any place"

    the command is :
    java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator scores -R genome.fa -known maize_snps_v3.vcf -I input_merged_lane_sorted_dedup.bam -o input_merged_lane_sorted_dedup_intervals

    Using GATK v3.5

    Post edited by medhat on

    Issue · Github
    by Sheila

    Issue Number
    Last Updated
    Closed By
  • SheilaSheila Broad InstitutePosts: 4,090Member, Broadie, Moderator, Dev admin


    It looks like that link should be:


  • medhatmedhat PolandPosts: 13Member

    thanks a lot it was fixed by adding flag --fix_misencoded_quality_score

  • SheilaSheila Broad InstitutePosts: 4,090Member, Broadie, Moderator, Dev admin

    Great. I just made a note to fix the error message so it points to the correct article :smile:

  • daxuedaxue Posts: 2Member

    The link to Step-by-step tutorial(s), (howto) Perform local realignment around indels, is broken: . Some other howto links also not working. Could you please fix it? Thanks.

  • daxuedaxue Posts: 2Member

    The link is in Best Practice -> Pre-processing -> Realign Indels.

  • SheilaSheila Broad InstitutePosts: 4,090Member, Broadie, Moderator, Dev admin


    I suspect those are being fixed as we talk on the thread! :smiley:

    As for the how to, here it is. This new article replaces the old article (2800).


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,557Administrator, Dev admin

    Yes this is actually fixed in web dev, and we'll be pushing the updates later this week following the 3.6 release (which is happening today).

    Geraldine Van der Auwera, PhD

  • CardiffBioinfCardiffBioinf CardiffPosts: 3Member

    Dear GATK team

    I was hoping you could advise how to resolve the 54bp deletion in the attached screen shot. This data is from a tumour-only amplicon experiment. It actually does get called with HaplotypeCaller but I understand it's not really suitable to use the local reassembly tool with low complexity data, is that correct? So I've been trying to force IR to resolve it by manipulating the LOD, greedy and max consensuses values but the gap wont open. I have checked the region is included in the interval file.

    Any thoughts or suggestions much appreciated.


    Screen Shot 2016-10-10 at 14.38.02.png
    2672 x 1186 - 97K
  • SheilaSheila Broad InstitutePosts: 4,090Member, Broadie, Moderator, Dev admin

    Hi Matt,

    For tumor data, you should be using MuTect2.


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