Local Realignment around Indels

delangeldelangel Posts: 71Dev mod
edited September 2012 in Methods and Algorithms

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 -Djava.io.tmpdir=/path/to/tmpdir \
  -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 Geraldine_VdAuwera on


  • medhatmedhat PolandPosts: 6Member
    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 https://www.broadinstitute.org/gatk/guide?id=6470 for more details and options related to this error. Any IDea?? "this link does not take me to any place"

    the command is :
    java -Djava.io.tmpdir=./temp/ -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
  • SheilaSheila Broad InstitutePosts: 3,222Member, Broadie, Moderator, Dev admin


    It looks like that link should be: https://www.broadinstitute.org/gatk/guide/article?id=6470


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