| java -jar GenomeAnalysisTK.jar |
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 |
Compare callability statistics |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R reference.fasta -o file_name_base -I input_bams.list [-geneList refSeq.sorted.txt] [-pt readgroup] [-ct 4 -ct 6 -ct 10] [-L my_capture_genes.interval_list] |
Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library |
| java -jar GenomeAnalysisTK.jar |
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 |
Extract specific fields from a VCF file to a tab-delimited table |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountTerminusEvent -R reference.fasta -I input.bam -o output.txt [-L input.intervals] |
Count the number of reads ending in insertions, deletions or soft-clips |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf |
Calculate genotype posterior likelihoods given panel data |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SplitSamFile -R reference.fasta -I input.bam --outputRoot myproject_ |
Split a BAM file by sample |
| GIREMI |
giremi [options] in1.bam [in2.bam [...]] |
GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R reference.fasta -T LeftAlignIndels -I reads.bam -o output_with_leftaligned_indels.bam |
Left-align indels within reads in a bam file |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T RegenotypeVariants -R reference.fasta --variant input.vcf -o output.vcf |
Regenotypes the variants from a VCF containing PLs or GLs. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 |
Set the mapping quality of reads with a given value to another given value |
| java -jar GenomeAnalysisTK.jar |
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 |
Analyze coverage distribution and validate read mates per interval and per sample |
| GEMINI region |
gemini region --reg chr1:100-200 my.db |
Extracting variants from specific regions. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R reference.fasta -I my_file.bam [-cov 10 \] [-uncovered \] -o output.list |
Outputs a list of intervals that are covered to or above a given threshold |
| GEMINI region |
gemini region --gene PTPN22 my.db |
Extracting variants from specific genes. |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CombineGVCFs -R reference.fasta --variant sample1.g.vcf --variant sample2.g.vcf -o cohort.g.vcf |
Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T QualifyMissingIntervals -R reference.fasta -I input.bam -o output.grp -L input.intervals -cds cds.intervals -targets targets.intervals |
Collect quality metrics for a set of intervals |
| 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 -irn -iln |
Selects headers from a VCF source |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountIntervals -R reference.fasta -o output.txt -check intervals.list |
Count contiguous regions in an interval list |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T FlagStat -R reference.fasta -I reads.bam [-o output.txt] |
Collect statistics about sequence reads based on their SAM flags |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T HaplotypeResolver -R reference.fasta -V:v1 input1.vcf -V:v2 input2.vcf -o output.vcf |
Haplotype-based resolution of variants in separate callsets. |