| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R reference.fasta -T ASEReadCounter -o file_name.csv -I input.bam -sites sites.vcf -U ALLOW_N_CIGAR_READS [-minDepth 10] [--minMappingQuality 10] [--minBaseQuality 2] [-drf DuplicateRead] |
Calculate read counts per allele for allele-specific expression analysis |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V hapmap.vcf --discordance myCalls.vcf -o output.vcf -sn mySample |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -fraction 0.5 |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ClipReads -R reference.fasta -I original.bam -o clipped.bam -XF seqsToClip.fasta -X CCCCC -CT "1-5,11-15" -QT 10 |
Read clipping based on quality, position or sequence matching |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf -o output.vcf -se 'SAMPLE.+PARC' -select "QD > 10.0" -invertSelect |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V NA12878.wgs.HC.vcf -supporting 1000G_EUR.genotypes.combined.vcf -o NA12878.wgs.HC.posteriors.vcf |
Calculate genotype posterior likelihoods given panel data |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ReadBackedPhasing -R reference.fasta -I reads.bam --variant SNPs.vcf -L SNPs.vcf -o phased_SNPs.vcf --phaseQualityThresh 20.0 |
Annotate physical phasing information |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ContEst -R reference.fasta -I:eval tumor.bam -I:genotype normal.bam --popFile populationAlleleFrequencies.vcf -L populationSites.interval_list [-L targets.interval_list] -isr INTERSECTION -o output.txt |
Estimate cross-sample contamination |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta --variant:foo input1.vcf --variant:bar input2.vcf -o output.vcf -genotypeMergeOptions PRIORITIZE -priority foo,bar |
Combine variant records from different sources |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CallableLoci -R reference.fasta -I myreads.bam -summary table.txt -o callable_status.bed |
Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome |
| 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 -he '.*SnpEff.*' |
Selects headers from a VCF source |
| java -jar GenomeAnalysisTK.jar |
Java -jar GenomeAnalysisTK.jar -T VariantEval -R reference.fasta -o output.MVs.byFamily.table --eval multiFamilyCallset.vcf -noEV -noST -ST Family -EV MendelianViolationEvaluator |
General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta --variant input1.vcf --variant input2.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY |
Combine variant records from different sources |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantAnnotator -I input.bam -V input.vcf -o output.vcf -L input.vcf --resource:foo resource.vcf -E foo.AF --resourceAlleleConcordance |
Annotate variant calls with context information |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignMappingQuality -DMQ 35 |
Set the mapping quality of all reads to a given value |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf -o output.vcf -xl_sn SAMPLE_1_PARC -xl_sn SAMPLE_1_ACTG -xl_se 'SAMPLE.+PARC' |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -Xmx2g -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants --variant input.vcf -o output.vcf --selectTypeToExclude INDEL |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R reference.fasta --variant sample1.g.vcf --variant sample2.g.vcf -o output.vcf |
Perform joint genotyping on gVCF files produced by HaplotypeCaller |
| java -jar GenomeAnalysisTK.jar |
java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R reference.fasta -input raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -recalFile output.recal -tranchesFile output.tranches -rscriptFile output.plots.R |
Build a recalibration model to score variant quality for filtering purposes |
| java -jar GenomeAnalysisTK.jar |
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 |
Annotate variant calls with context information |