Genome Variant Analysis

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: Analyze coverage distribution and validate read mates per interval and per sample

Usage: java -jar GenomeAnalysisTK.jar -T DiagnoseTargets -R reference.fasta -I sample1.bam -I sample2.bam -I sample3.bam -L intervals.interval_list -o output.vcf

Function: Extracting variants from specific genes.

Usage: gemini region --gene PTPN22 my.db

Function: Randomly select variant records according to specified options

Usage: 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

Function: Calculate basic statistics about the reference sequence itself

Usage: java -jar GenomeAnalysisTK.jar -T FastaStats -R reference.fasta [-o output.txt]

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: for comparison purposes, it's very useful to normalize the vcf output, especially for more complex graphs which can make large variant blocks that contain a lot of reference bases (Note: requires [vt](http://genome.sph.umich.edu/wiki/Vt)):

Usage: vt decompose_blocksub -a calls.vcf | vt normalize -r FASTA_FILE - > calls.clean.vcf

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: 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 --splitMultiallelics

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: Left-align indels within reads in a bam file

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T LeftAlignIndels -I reads.bam -o output_with_leftaligned_indels.bam

Function: Left-align indels in a variant callset

Usage: java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --dontTrimAlleles

Function: Create plots to visualize base recalibration results

Usage: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I myinput.bam -knownSites bundle/my-trusted-snps.vcf \ # optional but recommended -knownSites bundle/my-trusted-indels.vcf \ # optional but recommended -o firstpass.table # Generate the second pass recalibration table file java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I myinput.bam -knownSites bundle/my-trusted-snps.vcf -knownSites bundle/my-trusted-indels.vcf -BQSR firstpass.table -o secondpass.table # Finally generate the plots and also keep a copy of the csv (optional) java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R reference.fasta -before firstpass.table -after secondpass.table -csv BQSR.csv \ # optional -plots BQSR.pdf

Function: Select a subset of variants from a larger callset

Usage: java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf --maxFilteredGenotypes 5 --minFilteredGenotypes 2 --maxFractionFilteredGenotypes 0.60 --minFractionFilteredGenotypes 0.10