40 lines
2.4 KiB
Markdown
40 lines
2.4 KiB
Markdown
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## Local Realignment around Indels
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http://gatkforums.broadinstitute.org/gatk/discussion/38/local-realignment-around-indels
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<h4>For a discussion of the implications of removing indel realignment from workflows, see <a href="http://gatkforums.broadinstitute.org/gatk/discussion/7847">Blog#7847</a> from June 2016.</h4>
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<hr />
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<h2>Realigner Target Creator </h2>
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<p>For a complete, detailed argument reference, refer to the GATK document page <a rel="nofollow" class="external text" href="http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_RealignerTargetCreator.html">here</a>.
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</p><p><br />
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</p>
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<h2>Indel Realigner</h2>
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<p>For a complete, detailed argument reference, refer to the GATK document page <a rel="nofollow" class="external text" href="http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_IndelRealigner.html">here</a>.
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</p><p><br />
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</p>
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<hr />
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<h1>Running the Indel Realigner only at known sites</h1>
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<p>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.
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</p><p>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.
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</p>
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<pre>
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java -Xmx1g -jar /path/to/GenomeAnalysisTK.jar \
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-T RealignerTargetCreator \
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-R /path/to/reference.fasta \
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-o /path/to/output.intervals \
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-known /path/to/indel_calls.vcf
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</pre>
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<p>The IndelRealigner step needs to be run on every bam file.
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</p>
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<pre>
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java -Xmx4g -Djava.io.tmpdir=/path/to/tmpdir \
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-jar /path/to/GenomeAnalysisTK.jar \
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-I <lane-level.bam> \
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-R <ref.fasta> \
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-T IndelRealigner \
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-targetIntervals <intervalListFromStep1Above.intervals> \
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-o <realignedBam.bam> \
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-known /path/to/indel_calls.vcf
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--consensusDeterminationModel KNOWNS_ONLY \
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-LOD 0.4
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</pre>
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