Closed syansanofi closed 3 years ago
This line should probably be changed to the following:
gatk --java-options $javaOptions Mutect2 -I $controlBam -I $bam -normal $controlSampleName -R $refGenome -L $bed -pon $panelOfNormal --germline-resource $germlineResource --bam-output $bamout --f1r2-tar-gz ${f1r2.tar.gz} -O $vcf
Refs https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2
New template for PileupSummaries tool. This tool should produce pileup tables used in CalculateContamination tool.
gatk --java-options $javaOptions GetPileupSummaries -I $bam -L $bed -R $refGenome -V $contaminationVCF --sequence-dictionary $sequenceDictionary --interval-set-rule INTERSECTION -O $tumorPileupTable
New template for CalculateContamination tool. This tool is a spiritual replacement for ContEst in older gatk versions.
--tumor-segmentation
was not included in early gatk4 versions but has reappeared, some documentation could have this discrepancy. gatk --java-options $javaOptions CalculateContamination -I $tumorPileupTable -L $bed --tumor-segmentation $segmentsTable -O $contaminationTable
SortSam applied to bamout of mutect2 for later stages.
gatk --java-options $javaOptions SortSam -I $bamout -O $bamoutSorted -SO coordinate
New template for LearnReadOrientationModel.
${f1r2.tar.gz}
gatk --java-options $javaOptions LearnReadOrientationModel -I ${f1r2.tar.gz} -O ${artifactsPriors.tar.gz}
New template for FilterMutectCalls.
-R
-V
-O
--contamination-table
--tumor-segmentation
--ob-priors
-stats
--filtering-stats
gatk --java-options $javaOptions FilterMutectCalls -R $refGenome -V $vcf -O $filteredVCF --contamination-table $contaminationTable --tumor-segmentation $segmentsTable --ob-priors ${artifactsPriors.tar.gz} -stats $vcfStats --filtering-stats $filteringStats
New template for FilterAlignmentArtifacts. Further filtering after FilterMutectCalls.
gatk --java-options $javaOptions FilterAlignmentArtifacts -I $bamoutSorted -V $filteredVCF -O $filteredVCFartifacts -R $refGenome --bwa-mem-index-image $bwaImage`
Issue
Update Mutect2 variant calling to include latest gatk (4.2.0.0) recommended best practices.
Approach
Related to this change, additional germline references are required (many are seen in mutect1 list, however not all are listed)
Important Points