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Function: Create plots to visualize base recalibration results
Usage: java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R myrefernce.fasta -before recal2.table -after recal3.table -plots recalQC.pdf
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Function: Compute the read error rate per position
Usage: java -jar GenomeAnalysisTK.jar -T ErrorRatePerCycle -R reference.fasta -I my_sequence_reads.bam -o error_rates.gatkreport.txt
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Function: Call variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair.
Usage: java -jar VarScan.jar copynumber [normal_pileup] [tumor_pileup] [output] OPTIONS
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Function: Find variants meeting an autosomal recessive model
Usage: gemini autosomal_recessive test.auto_rec.db --columns "chrom,start,end,gene"
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Function: Performs set-comparison operations on two files of variants.
Usage: java -jar VarScan.jar compare [file1] [file2] [type] [output] OPTIONS
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Function: Validate a VCF file with an extra strict set of criteria
Usage: java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --validationTypeToExclude ALLELES
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Function: Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles.
Usage: java -jar GenomeAnalysisTK.jar -T VariantsToAllelicPrimitives -R reference.fasta -V input.vcf -o output.vcf
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Function: Generate an alternative reference sequence over the specified interval
Usage: gatk FastaAlternateReferenceMaker [options] -R reference.fasta -O output.fasta -L input.intervals -V input.vcf
Supported input format:
VCF
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Function: Count the number of bases in a set of reads
Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T CountBases -I input.bam [-L input.intervals]
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Function: Define intervals to target for local realignment
Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam --known indels.vcf -o forIndelRealigner.intervals
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Function: Create plots to visualize base recalibration results
Usage: java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R myrefernce.fasta -ignoreLMT -BQSR recal1.table \ # you can discard any two -before recal2.table -after recal3.table -plots myrecals.pdf
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Function: Compare GATK's internal pileup to a reference Samtools pileup
Usage: java -jar GenomeAnalysisTK.jar -T CheckPileup -R reference.fasta -I your_data.bam --pileup:SAMPileup pileup_file.txt -L chr1:257-275 -o output_file_name
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Function: Count the number of reads seen from male samples
Usage: java -jar GenomeAnalysisTK.jar -T CountMales -R reference.fasta -I samples.bam -o output.txt
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Function: Validate a VCF file with an extra strict set of criteria
Usage: java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --validationTypeToExclude ALL
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Function: Randomly split variants into different sets
Usage: java -jar GenomeAnalysisTK.jar -T RandomlySplitVariants -R reference.fasta -V input.vcf -o1 output_1.vcf -o2 output_2.vcf