| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T FastaReferenceMaker -R reference.fasta -o output.fasta -L input.intervals |
Create a subset of a FASTA reference sequence |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -selectType INDEL --minIndelSize 2 --maxIndelSize 5 |
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 -L /path/to/my.interval_list -sn SAMPLE_1_ACTG |
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 -selectType SNP -selectType MNP -restrictAllelesTo MULTIALLELIC |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ApplyRecalibration -R reference.fasta -input raw_variants.withASannotations.vcf -AS --ts_filter_level 99.0 -tranchesFile output.AS.tranches -recalFile output.AS.recal -mode SNP -o path/to/output.recalibrated.ASfiltered.vcf |
Apply a score cutoff to filter variants based on a recalibration table |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf --skipPopulationPriors -ped family.ped -o output.withPosteriors.vcf |
Calculate genotype posterior likelihoods given panel data |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R reference.fasta -V input.vcf -o output.withPosteriors.vcf --ignoreInputSamples |
Calculate genotype posterior likelihoods given panel data |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V myCalls.vcf --concordance theirCalls.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 -ped family.ped -mv -mvq 50 -o violations.vcf |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table |
Detect systematic errors in base quality scores |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ContEst -R reference.fasta -I tumor.bam --genotypes normalGenotypes.vcf --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 -Xmx2g -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -se 'SAMPLE.+PARC' -select "QD > 10.0" |
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 -ped family.ped -mv -mvq 50 -invMv -o violations.vcf |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants -R reference.fasta -V input1.vcf -V input2.vcf -out output.vcf -assumeSorted |
Concatenate VCF files of non-overlapping genome intervals, all with the same set of samples |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fasta -I input.bam -o raw_variants.vcf --output_mode EMIT_ALL_SITES |
Call SNPs and indels on a per-locus basis |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T VariantEval -R reference.fasta -o output.eval.grp --eval:set1 set1.vcf --eval:set2 set2.vcf [--comp comp.vcf] |
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 ApplyRecalibration -R reference.fasta -input raw_variants.vcf --ts_filter_level 99.0 -tranchesFile output.tranches -recalFile output.recal -mode SNP -o path/to/output.recalibrated.filtered.vcf |
Apply a score cutoff to filter variants based on a recalibration table |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_A_PARC -sn SAMPLE_B_ACTG |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R ref.fasta -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_1_ACTG -env -ef |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T VariantFiltration -R reference.fasta -o output.vcf --variant input.vcf --filterExpression "AB 50" --filterName "SomeFilterName" |
Filter variant calls based on INFO and FORMAT annotations |