Genome Variant Analysis

Function: Annotate variant calls with context information

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantAnnotator -I input.bam -V input.vcf -o output.vcf -A Coverage -L input.vcf --dbsnp dbsnp.vcf

Function: Compare callability statistics

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T CompareCallableLoci -comp1 callable_loci_1.bed -comp2 callable_loci_2.bed [-L input.intervals \] -o comparison.table

Function: Count the number of reads ending in insertions, deletions or soft-clips

Usage: java -jar GenomeAnalysisTK.jar -T CountTerminusEvent -R reference.fasta -I input.bam -o output.txt [-L input.intervals]

Function: Split a BAM file by sample

Usage: java -jar GenomeAnalysisTK.jar -T SplitSamFile -R reference.fasta -I input.bam --outputRoot myproject_

Function: Extract specific fields from a VCF file to a tab-delimited table

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantsToTable -V file.vcf -F CHROM -F POS -F ID -F QUAL -F AC -o results.table

Function: Calculate genotype posterior likelihoods given panel data

Usage: java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf

Function: Set the mapping quality of reads with a given value to another given value

Usage: java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60

Function: GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

Usage: giremi [options] in1.bam [in2.bam [...]]

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: Regenotypes the variants from a VCF containing PLs or GLs.

Usage: java -jar GenomeAnalysisTK.jar -T RegenotypeVariants -R reference.fasta --variant input.vcf -o output.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: Extracting variants from specific regions.

Usage: gemini region --reg chr1:100-200 my.db

Function: Outputs a list of intervals that are covered to or above a given threshold

Usage: java -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R reference.fasta -I my_file.bam [-cov 10 \] [-uncovered \] -o output.list

Function: Extracting variants from specific genes.

Usage: gemini region --gene PTPN22 my.db

Function: Count contiguous regions in an interval list

Usage: java -jar GenomeAnalysisTK.jar -T CountIntervals -R reference.fasta -o output.txt -check intervals.list