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mkatari-bioinformatics-august-2013-gatknotes [2016/08/10 20:45] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2016/08/10 20:47] – mkatari
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    -targetIntervals Sample1forIndelRealigner.intervals \    -targetIntervals Sample1forIndelRealigner.intervals \
    -o Sample1.dedup.realign.bam    -o Sample1.dedup.realign.bam
 +
 +GenomeAnalysisTK \
 +   -T RealignerTargetCreator \
 +   -R PTC_Human.fasta \
 +   -I Sample2.dedup.bam \
 +   -o Sample2forIndelRealigner.intervals 
 +
 +GenomeAnalysisTK \
 +   -T IndelRealigner \
 +   -R PTC_Human.fasta \
 +   -I Sample2.dedup.bam \
 +   -targetIntervals Sample2forIndelRealigner.intervals \
 +   -o Sample2.dedup.realign.bam
 +
 +
 +GenomeAnalysisTK \
 +   -T RealignerTargetCreator \
 +   -R PTC_Human.fasta \
 +   -I Sample3.dedup.bam \
 +   -o Sample3forIndelRealigner.intervals
 + 
 +GenomeAnalysisTK \
 +   -T IndelRealigner \
 +   -R PTC_Human.fasta \
 +   -I Sample3.dedup.bam \
 +   -targetIntervals Sample3forIndelRealigner.intervals \
 +   -o Sample3.dedup.realign.bam
 +
 +GenomeAnalysisTK \
 +   -T RealignerTargetCreator \
 +   -R PTC_Human.fasta \
 +   -I Sample4.dedup.bam \
 +   -o Sample4forIndelRealigner.intervals
 + 
 +
 +GenomeAnalysisTK \
 +   -T IndelRealigner \
 +   -R PTC_Human.fasta \
 +   -I Sample4.dedup.bam \
 +   -targetIntervals Sample4forIndelRealigner.intervals \
 +   -o Sample4.dedup.realign.bam
  
 </code> </code>
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari