-
Function: Selects headers from a VCF source
Usage: java -jar GenomeAnalysisTK.jar -T SelectHeaders -R reference.fasta -V input.vcf -o output.vcf -hn FILTER -hn FORMAT -hn INFO -irn -iln
-
Function: Collect quality metrics for a set of intervals
Usage: java -jar GenomeAnalysisTK.jar -T QualifyMissingIntervals -R reference.fasta -I input.bam -o output.grp -L input.intervals -cds cds.intervals -targets targets.intervals
-
Function: Collect statistics about sequence reads based on their SAM flags
Usage: java -jar GenomeAnalysisTK.jar -T FlagStat -R reference.fasta -I reads.bam [-o output.txt]
-
Function: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file
Usage: java -jar GenomeAnalysisTK.jar -T CombineGVCFs -R reference.fasta --variant sample1.g.vcf --variant sample2.g.vcf -o cohort.g.vcf
-
Function: Haplotype-based resolution of variants in separate callsets.
Usage: java -jar GenomeAnalysisTK.jar -T HaplotypeResolver -R reference.fasta -V:v1 input1.vcf -V:v2 input2.vcf -o output.vcf
-
Function: Left-align indels in a variant callset
Usage: java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --splitMultiallelics
-
Function: Calculate basic statistics about the reference sequence itself
Usage: java -jar GenomeAnalysisTK.jar -T FastaStats -R reference.fasta [-o output.txt]
-
Function: Selects headers from a VCF source
Usage: java -jar GenomeAnalysisTK.jar -T SelectHeaders -R reference.fasta -V input.vcf -o output.vcf -hn FILTER -hn FORMAT -hn INFO
-
Function: Left-align indels in a variant callset
Usage: java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf
-
Function: Randomly select variant records according to specified options
Usage: 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
-
Function: Convert variants from other file formats to VCF format
Usage: java -jar GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fasta -o output.vcf --variant:RawHapMap input.hapmap
-
Function: Count the number of ROD objects encountered
Usage: java -jar GenomeAnalysisTK.jar -T CountRODs -R reference.fasta -o output.txt --rod input.vcf
-
Function: 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.
Usage: java -jar VarScan.jar somaticFilter [mutations file] OPTIONS
-
Function: Genotype concordance between two callsets
Usage: java -jar GenomeAnalysisTK.jar -T GenotypeConcordance -R reference.fasta -eval test_set.vcf -comp truth_set.vcf -o output.grp
-
Function: Find genes among variants that are interacting partners.
Usage: gemini interactions -g CTBP2 -r 3 example.db