| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --splitMultiallelics |
Left-align indels in a variant callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fasta -o output.vcf --variant:RawHapMap input.hapmap |
Convert variants from other file formats to VCF format |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T FastaStats -R reference.fasta [-o output.txt] |
Calculate basic statistics about the reference sequence itself |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf |
Left-align indels in a variant callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectHeaders -R reference.fasta -V input.vcf -o output.vcf -hn FILTER -hn FORMAT -hn INFO |
Selects headers from a VCF source |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ValidationSiteSelectorWalker -R reference.fasta -V input1.vcf -V input2.vcf -sn NA12878 -o output.vcf --numValidationSites 200 -sampleMode POLY_BASED_ON_GT -freqMode KEEP_AF_SPECTRUM |
Randomly select variant records according to specified options |
| GEMINI interactions |
gemini interactions -g CTBP2 -r 3 example.db |
Find genes among variants that are interacting partners. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountRODs -R reference.fasta -o output.txt --rod input.vcf |
Count the number of ROD objects encountered |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T GenotypeConcordance -R reference.fasta -eval test_set.vcf -comp truth_set.vcf -o output.grp |
Genotype concordance between two callsets |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R myrefernce.fasta -BQSR myrecal.table -plots BQSR.pdf |
Create plots to visualize base recalibration results |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R reference.fasta -T CountBases -I input.bam [-L input.intervals] |
Count the number of bases in a set of reads |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero // Prints the first 2000 reads in the BAM file java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.bam -n 2000 // Downsamples BAM file to 25% java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.bam -dfrac 0.25 |
Write out sequence read data (for filtering, merging, subsetting etc) |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf --maxFilteredGenotypes 5 --minFilteredGenotypes 2 --maxFractionFilteredGenotypes 0.60 --minFractionFilteredGenotypes 0.10 |
Select a subset of variants from a larger callset |
| VarScan |
java -jar VarScan.jar copynumber [normal_pileup] [tumor_pileup] [output] OPTIONS |
Call variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair. |
| VarScan |
java -jar VarScan.jar somaticFilter [mutations file] OPTIONS |
Filter somatic mutation calls to remove clusters of false positives and SNV calls near indels. Note: this is a basic filter. More advanced filtering strategies consider mapping quality, read mismatches, soft-trimming, and other factors when deciding whether or not to filter a variant. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ErrorRatePerCycle -R reference.fasta -I my_sequence_reads.bam -o error_rates.gatkreport.txt |
Compute the read error rate per position |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --dontTrimAlleles |
Left-align indels in a variant callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ValidationSiteSelectorWalker -R reference.fasta -V:foo input1.vcf -V:bar input2.vcf --numValidationSites 200 -sf samples.txt -o output.vcf -sampleMode POLY_BASED_ON_GT -freqMode UNIFORM -selectType INDEL |
Randomly select variant records according to specified options |
| GEMINI autosomal_dominant |
gemini autosomal_dominant test.auto_dom.db --columns "chrom,start,end,gene" |
Find variants meeting an autosomal dominant model. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --splitMultiallelics --dontTrimAlleles --keepOriginalAC |
Left-align indels in a variant callset |