ILRI Research Computing

User Tools

Site Tools

You are here: start » mkatari-bioinformatics-august-2013-gatknotes
mkatari-bioinformatics-august-2013-gatknotes

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatarimkatari-bioinformatics-august-2013-gatknotes [2015/06/08 07:45] – mkatari
Line 40: Line 40:
 </code> </code>
  
-The picard method to sort is preferred by GATK+The picard method to sort is preferred by GATK. In some cases PICARD uses the temp directory to do its sorting. You may run into an error that complains about running out of space. To avoid this problem simply create your own tmp directory and tell java that it should use it. See details [[https://www.biostars.org/p/42613/|here]]. 
 <code> <code>
-java -jar /export/apps/picard-tools/1.112/SortSam.jar \+mkdir /var/scratch/mkatari 
 +mkdir /var/scratch/mkatari/tmp 
 + 
 +java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/SortSam.jar \
    INPUT=Cohen.bam \    INPUT=Cohen.bam \
    OUTPUT=Cohen.sorted.bam \    OUTPUT=Cohen.sorted.bam \
Line 54: Line 58:
 <code> <code>
  
-java -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \+java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/AddOrReplaceReadGroups.jar \
    INPUT=Cohen.sorted.bam \    INPUT=Cohen.sorted.bam \
    OUTPUT=CohenRG.bam \    OUTPUT=CohenRG.bam \
Line 65: Line 69:
 This will remove any reads that map to the same exact place. It is helpful to get rid of artifacts.  This will remove any reads that map to the same exact place. It is helpful to get rid of artifacts. 
 <code> <code>
-java -jar /export/apps/picard-tools/1.112/MarkDuplicates.jar \+ 
 +java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/MarkDuplicates.jar \
    INPUT=CohenRG.bam \    INPUT=CohenRG.bam \
    OUTPUT=Cohen.dedup.bam \    OUTPUT=Cohen.dedup.bam \
    METRICS_FILE=Cohen.dedup.metrics \    METRICS_FILE=Cohen.dedup.metrics \
    REMOVE_DUPLICATES=TRUE \    REMOVE_DUPLICATES=TRUE \
-   ASSUME_SORTED=TRUE+   ASSUME_SORTED=TRUE \ 
 +   MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000
  
 </code> </code>
Line 79: Line 85:
  
 #identifying indels #identifying indels
-java -Xmx2g -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+java -Xmx2g -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \
    -T RealignerTargetCreator \    -T RealignerTargetCreator \
    -R PTC_Human.fasta \    -R PTC_Human.fasta \
Line 87: Line 93:
  
    
- java -Xmx4g -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+ 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 \
Line 99: Line 105:
  
 <code> <code>
-java -jar /export/apps/picard-tools/1.112/CleanSam.jar \+java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/CleanSam.jar \
    INPUT=Sherman.dedup.realign.bam \    INPUT=Sherman.dedup.realign.bam \
    OUTPUT=Sherman.clean.dedup.realign.bam    OUTPUT=Sherman.clean.dedup.realign.bam
Line 107: Line 113:
  
 <code> <code>
-java -jar /export/apps/picard-tools/1.112/MergeSamFiles.jar \+java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/picard-tools/1.112/MergeSamFiles.jar \
    INPUT=Sherman.clean.dedup.realign.bam \    INPUT=Sherman.clean.dedup.realign.bam \
    INPUT=Cohen.dedup.realign.bam \    INPUT=Cohen.dedup.realign.bam \
Line 121: Line 127:
  
 <code> <code>
-java -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+java -Djava.io.tmpdir=/var/scratch/mkatari/tmp -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \
    -T UnifiedGenotyper \    -T UnifiedGenotyper \
    -I ShermanCohenMerged.sorted.bam \    -I ShermanCohenMerged.sorted.bam \
Line 140: Line 146:
 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 -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \+java --Djava.io.tmpdir=/var/scratch/mkatari/tmp jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \
      -R PTC_Human.fasta      -R PTC_Human.fasta
      -T VariantsToTable \      -T VariantsToTable \
Line 147: Line 153:
      -GF GT -GF GQ \      -GF GT -GF GQ \
      -o PTC_human.gatk.vcf.table      -o PTC_human.gatk.vcf.table
 +</code>
 +
 +In order to filter your vcf file based on quality measures, depth, and also statistical significance, you can use variant filter option in the gatk toolkit. Below is an example of suggested filters for data that has low coverage.
 +
 +<code>
 +java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \
 +    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa \
 +    -T VariantFiltration \
 +    -o namikonga_albert_filter.vcf \
 +    --variant /home/emasumba/Namikonga_Albert.gatk.vcf \
 +    --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore >13.0" \
 +    --filterName "mannyfilter"
 +
 +</code>
 +
 +Good descriptions of the different information on vcf files [[https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_HaplotypeScore.php|GATK Docs]]
 +
 +Finally to save the SNPs that passed your filter, you simply use the selectvariant tool.
 +
 +<code>
 +
 +java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \
 +    -T SelectVariants \
 +    --variant namikonga_albert_filter.vcf \
 +    -o namikonga_albert_filter_only.vcf \
 +    -ef \
 +    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa
 +
 </code> </code>
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari