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mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 12:52] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2014/06/13 08:28] – mkatari
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   * create a bam index for dedup bam files   * create a bam index for dedup bam files
   * realign samples   * realign samples
 +
 +Once they are all processed
   * merge all samples to one bam file   * merge all samples to one bam file
   * sort and index this merged bam file   * sort and index this merged bam file
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 bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam
 samtools view -bS Cohen.sam > Cohen.bam samtools view -bS Cohen.sam > Cohen.bam
-bowtie2 -x PTC_Human -U Sherman.fastq -S Sherman.sam 
-samtools view -bS Sherman.sam > Sherman.bam 
 </code> </code>
  
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    SORT_ORDER=coordinate    SORT_ORDER=coordinate
        
-java -jar /export/apps/picard-tools/1.112/SortSam.jar \ +
-   INPUT=Sherman.bam \ +
-   OUTPUT=Sherman.sorted.bam \ +
-   SORT_ORDER=coordinate+
 </code> </code>
  
Line 56: Line 53:
  
 <code> <code>
-java -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \ 
-   INPUT=Sherman.sorted.bam \ 
-   OUTPUT=ShermanRG.bam \ 
-   RGLB=Sherman \ 
-   RGPL=IonTorrent \ 
-   RGPU=None \ 
-   RGSM=Sherman 
  
 java -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \ java -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \
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    ASSUME_SORTED=TRUE    ASSUME_SORTED=TRUE
  
-java -jar /export/apps/picard-tools/1.112/MarkDuplicates.jar \ 
-   INPUT=ShermanRG.bam \ 
-   OUTPUT=Sherman.dedup.bam \ 
-   METRICS_FILE=Sherman.dedup.metrics \ 
-   REMOVE_DUPLICATES=TRUE \ 
-   ASSUME_SORTED=TRUE 
 </code> </code>
  
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 <code> <code>
 samtools index Cohen.dedup.bam  samtools index Cohen.dedup.bam 
-samtools index Sherman.dedup.bam  
  
 #identifying indels #identifying indels
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    -o CohenforIndelRealigner.intervals    -o CohenforIndelRealigner.intervals
    
- #identifying indels 
-java -Xmx2g -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \ 
-   -T RealignerTargetCreator \ 
-   -R PTC_Human.fasta \ 
-   -I Sherman.dedup.bam \ 
-   -o ShermanforIndelRealigner.intervals 
  
    
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   -targetIntervals CohenforIndelRealigner.intervals \   -targetIntervals CohenforIndelRealigner.intervals \
    -o Cohen.dedup.realign.bam    -o Cohen.dedup.realign.bam
- 
- java -Xmx4g -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \ 
-   -T IndelRealigner \ 
-   -R PTC_Human.fasta \ 
-   -I Sherman.dedup.bam \ 
-  -targetIntervals ShermanforIndelRealigner.intervals \ 
-   -o Sherman.dedup.realign.bam 
  
 </code> </code>
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    -glm SNP \    -glm SNP \
    -o PTC_human.gatk.vcf    -o PTC_human.gatk.vcf
 +
 +</code>
 +
 +If you want to load the vcf file into IGV, remember to index it first.
 +<code>
 +module load igvtools
 +igvtools index PTC_human.gatk.vcf
 +</code>
 +
 +If you would like to generate a table of from the vcf file use the following command
 +<code>
 +java -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \
 +     -R PTC_Human.fasta
 +     -T VariantsToTable \
 +     -V PTC_human.gatk.vcf \
 +     -F CHROM -F POS -F ID -F QUAL -F AC \
 +     -GF GT -GF GQ \
 +     -o PTC_human.gatk.vcf.table
 </code> </code>
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari