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mkatari-bioinformatics-august-2013-gatknotes [2015/06/08 07:45] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2016/08/10 20:45] – mkatari
Line 36: Line 36:
  
 <code> <code>
-bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam +bowtie2 -x PTC_Human -U Sample1.fastq -S Sample1.sam 
-samtools view -bS Cohen.sam > Cohen.bam+samtools view -bS Sample1.sam > Sample1.bam 
 + 
 +bowtie2 -x PTC_Human -U Sample2.fastq -S Sample2.sam 
 +samtools view -bS Sample2.sam > Sample2.bam 
 + 
 +bowtie2 -x PTC_Human -U Sample3.fastq -S Sample3.sam 
 +samtools view -bS Sample3.sam > Sample3.bam 
 + 
 +bowtie2 -x PTC_Human -U Sample4.fastq -S Sample4.sam 
 +samtools view -bS Sample4.sam > Sample4.bam
 </code> </code>
  
Line 43: Line 52:
  
 <code> <code>
-mkdir /var/scratch/mkatari +module load picard/1.133 
-mkdir /var/scratch/mkatari/tmp+ 
 +picard SortSam INPUT=Sample1.bam OUTPUT=Sample1.sorted.bam \ 
 +    SORT_ORDER=coordinate 
 + 
 +picard SortSam INPUT=Sample2.bam OUTPUT=Sample2.sorted.bam \ 
 +    SORT_ORDER=coordinate 
 + 
 +picard SortSam INPUT=Sample3.bam OUTPUT=Sample3.sorted.bam \ 
 +    SORT_ORDER=coordinate 
 + 
 +picard SortSam INPUT=Sample4.bam OUTPUT=Sample4.sorted.bam \ 
 +    SORT_ORDER=coordinate
  
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/SortSam.jar \ 
-   INPUT=Cohen.bam \ 
-   OUTPUT=Cohen.sorted.bam \ 
-   SORT_ORDER=coordinate 
-    
  
 </code> </code>
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 <code> <code>
 +picard AddOrReplaceReadGroups \
 +   INPUT=Sample1.sorted.bam \
 +   OUTPUT=Sample1RG.bam \
 +   RGLB=Sample1 \
 +   RGPL=IonTorrent \
 +   RGPU=None \
 +   RGSM=Sample1
  
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \ +picard AddOrReplaceReadGroups \ 
-   INPUT=Cohen.sorted.bam \ +   INPUT=Sample2.sorted.bam \ 
-   OUTPUT=CohenRG.bam \ +   OUTPUT=Sample2RG.bam \ 
-   RGLB=Cohen \+   RGLB=Sample2 \
    RGPL=IonTorrent \    RGPL=IonTorrent \
    RGPU=None \    RGPU=None \
-   RGSM=Cohen+   RGSM=Sample2 
 + 
 +picard AddOrReplaceReadGroups \ 
 +   INPUT=Sample3.sorted.bam \ 
 +   OUTPUT=Sample3RG.bam \ 
 +   RGLB=Sample3 \ 
 +   RGPL=IonTorrent \ 
 +   RGPU=None \ 
 +   RGSM=Sample3 
 + 
 +picard AddOrReplaceReadGroups \ 
 +   INPUT=Sample4.sorted.bam \ 
 +   OUTPUT=Sample4RG.bam \ 
 +   RGLB=Sample4 \ 
 +   RGPL=IonTorrent \ 
 +   RGPU=None \ 
 +   RGSM=Sample4 
 + 
 </code> </code>
  
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 <code> <code>
  
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/MarkDuplicates.jar \ +picard MarkDuplicates \ 
-   INPUT=CohenRG.bam \ +   INPUT=Sample1RG.bam \ 
-   OUTPUT=Cohen.dedup.bam \ +   OUTPUT=Sample1.dedup.bam \ 
-   METRICS_FILE=Cohen.dedup.metrics \+   METRICS_FILE=Sample1.dedup.metrics \ 
 +   REMOVE_DUPLICATES=TRUE \ 
 +   ASSUME_SORTED=TRUE \ 
 +   MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 
 + 
 + 
 +picard MarkDuplicates \ 
 +   INPUT=Sample2RG.bam \ 
 +   OUTPUT=Sample2.dedup.bam \ 
 +   METRICS_FILE=Sample2.dedup.metrics \ 
 +   REMOVE_DUPLICATES=TRUE \ 
 +   ASSUME_SORTED=TRUE \ 
 +   MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 
 + 
 +picard MarkDuplicates \ 
 +   INPUT=Sample3RG.bam \ 
 +   OUTPUT=Sample3.dedup.bam \ 
 +   METRICS_FILE=Sample3.dedup.metrics \ 
 +   REMOVE_DUPLICATES=TRUE \ 
 +   ASSUME_SORTED=TRUE \ 
 +   MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 
 + 
 +picard MarkDuplicates \ 
 +   INPUT=Sample4RG.bam \ 
 +   OUTPUT=Sample4.dedup.bam \ 
 +   METRICS_FILE=Sample4.dedup.metrics \
    REMOVE_DUPLICATES=TRUE \    REMOVE_DUPLICATES=TRUE \
    ASSUME_SORTED=TRUE \    ASSUME_SORTED=TRUE \
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 Index the files and realign them Index the files and realign them
 <code> <code>
-samtools index Cohen.dedup.bam +samtools index Sample1.dedup.bam  
 +samtools index Sample2.dedup.bam  
 +samtools index Sample3.dedup.bam  
 +samtools index Sample4.dedup.bam 
  
 #identifying indels #identifying indels
-java -Xmx2g -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+ 
 +module load gatk/3.3.0 
 + 
 +GenomeAnalysisTK \
    -T RealignerTargetCreator \    -T RealignerTargetCreator \
    -R PTC_Human.fasta \    -R PTC_Human.fasta \
-   -I Cohen.dedup.bam \ +   -I Sample1.dedup.bam \ 
-   -o CohenforIndelRealigner.intervals+   -o Sample1forIndelRealigner.intervals
    
  
-  +GenomeAnalysisTK \
- java -Xmx4g -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+
    -T IndelRealigner \    -T IndelRealigner \
    -R PTC_Human.fasta \    -R PTC_Human.fasta \
-   -I Cohen.dedup.bam \ +   -I Sample1.dedup.bam \ 
-  -targetIntervals CohenforIndelRealigner.intervals \ +   -targetIntervals Sample1forIndelRealigner.intervals \ 
-   -o Cohen.dedup.realign.bam+   -o Sample1.dedup.realign.bam
  
 </code> </code>
Line 105: Line 175:
  
 <code> <code>
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/CleanSam.jar \ +picard CleanSam \ 
-   INPUT=Sherman.dedup.realign.bam \ +   INPUT=Sample4.dedup.realign.bam \ 
-   OUTPUT=Sherman.clean.dedup.realign.bam+   OUTPUT=Sample4.clean.dedup.realign.bam
 </code> </code>
  
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 <code> <code>
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/MergeSamFiles.jar \ +picard MergeSamFiles \ 
-   INPUT=Sherman.clean.dedup.realign.bam \ +   INPUT=Sample1.dedup.realign.bam \ 
-   INPUT=Cohen.dedup.realign.bam \ +   INPUT=Sample2.dedup.realign.bam \ 
-   OUTPUT=ShermanCohenMerged.bam  +   INPUT=Sample3.dedup.realign.bam \ 
 +   INPUT=Sample4.dedup.realign.bam \ 
 +   OUTPUT=AllMerged.bam   
 + 
 +picard SortSam INPUT=AllMerged.bam OUTPUT=AllMerged.sorted.bam SORT_ORDER=coordinate
  
-samtools sort ShermanCohenMerged.bam ShermanCohenMerged.sorted+samtools index AllMerged.sorted.bam
  
-samtools index ShermanCohenMerged.sorted.bam  
 </code> </code>
  
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 <code> <code>
-java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \ +GenomeAnalysisTK -T UnifiedGenotyper \ 
-   -T UnifiedGenotyper \ +   -I AllMerged.sorted.bam \
-   -I ShermanCohenMerged.sorted.bam \+
    -R PTC_Human.fasta \    -R PTC_Human.fasta \
    --output_mode EMIT_VARIANTS_ONLY \    --output_mode EMIT_VARIANTS_ONLY \
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 If you would like to generate a table of from the vcf file use the following command If you would like to generate a table of from the vcf file use the following command
 <code> <code>
-java --Djava.io.tmpdir=/var/scratch/mkatari/tmp jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+GenomeAnalysisTK \
      -R PTC_Human.fasta      -R PTC_Human.fasta
      -T VariantsToTable \      -T VariantsToTable \
Line 158: Line 230:
  
 <code> <code>
-java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \ +GenomeAnalysisTK \ 
-    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa \+    -R PTC_Human.fasta \
     -T VariantFiltration \     -T VariantFiltration \
-    -o namikonga_albert_filter.vcf \ +    -o PTC_human.gatk.filter.vcf \ 
-    --variant /home/emasumba/Namikonga_Albert.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"
Line 174: Line 246:
 <code> <code>
  
-java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \+GenomeAnalysisTK \
     -T SelectVariants \     -T SelectVariants \
-    --variant namikonga_albert_filter.vcf \ +    --variant PTC_human.gatk.filter.vcf \ 
-    -o namikonga_albert_filter_only.vcf \+    -o PTC_human.gatk.filter.only.vcf \
     -ef \     -ef \
-    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa+    -R PTC_Human.fasta
  
 </code> </code>
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari