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mkatari-bioinformatics-august-2013-gatknotes [2016/08/10 20:45] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2016/08/17 08:37] (current) – mkatari
Line 12: Line 12:
 module load bowtie2 module load bowtie2
 module load samtools module load samtools
 +module load picard
  
 bowtie2-build PTC_Human.fasta PTC_Human bowtie2-build PTC_Human.fasta PTC_Human
 samtools faidx PTC_Human.fasta samtools faidx PTC_Human.fasta
-java -jar /export/apps/picard-tools/1.112/CreateSequenceDictionary.jar \+picard CreateSequenceDictionary \
    R=PTC_Human.fasta \    R=PTC_Human.fasta \
    O=PTC_Human.dict    O=PTC_Human.dict
Line 169: Line 170:
    -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>
Line 219: Line 261:
 <code> <code>
 GenomeAnalysisTK \ GenomeAnalysisTK \
-     -R PTC_Human.fasta+     -R PTC_Human.fasta \
      -T VariantsToTable \      -T VariantsToTable \
      -V PTC_human.gatk.vcf \      -V PTC_human.gatk.vcf \
Line 235: Line 277:
     -o PTC_human.gatk.filter.vcf \     -o PTC_human.gatk.filter.vcf \
     --variant PTC_human.gatk.vcf \     --variant PTC_human.gatk.vcf \
-    --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore >13.0" \ +    --filterExpression "QD<2.0||MQ<40.0||FS>60.0||HaplotypeScore>13.0" \ 
-    --filterName "mannyfilter"+    --filterName mannyfilter
  
 </code> </code>
mkatari-bioinformatics-august-2013-gatknotes.1470861918.txt.gz · Last modified: 2016/08/10 20:45 by mkatari