Genome Variant Analysis

Function: Print read alignments in Pileup-style format

Usage: java -jar GenomeAnalysisTK.jar -T Pileup -R reference.fasta -I my_reads.bam -L chr1:257-267 -o output.txt

Function: Left-align indels in a variant callset

Usage: java -jar GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants -R reference.fasta --variant input.vcf -o output.vcf --reference_window_stop 208

Function: Collect read length statistics

Usage: java -jar GenomeAnalysisTK.jar -T ReadLengthDistribution -R reference.fasta -I example.bam -o example.tbl

Function: Generate simulated reads for variants

Usage: java -jar GenomeAnalysisTK.jar -T SimulateReadsForVariants -R reference.fasta -V input_variants.vcf -o simulated_reads.bam --readDepth 50 --errorRate 25

Function: Annotate variant calls with context information

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantAnnotator -V input.vcf -o output.vcf --resource:foo resource.vcf --expression foo.AF --expression foo.FILTER

Function: Call SNPs and indels on a per-locus basis

Usage: java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fasta -I sample1.bam [-I sample2.bam ...] --dbsnp dbSNP.vcf -o snps.raw.vcf -stand_call_conf [50.0] [-L targets.interval_list]

Function: Collect statistics about read groups and their properties

Usage: java -jar GenomeAnalysisTK.jar -T ReadGroupProperties -R reference.fasta -I example1.bam -I example2.bam -o readgroup_report.grp

Function: Identifying potential compound heterozygotes

Usage: gemini comp_hets my.db --columns "chrom, start, end" test.comp_het_default.2.db

Function: Count the number of reads

Usage: java -jar GenomeAnalysisTK.jar -R reference.fasta -T CountReads -I input.bam [-L input.intervals]

Function: Quality control for the reference fasta

Usage: java -jar GenomeAnalysisTK.jar -T QCRef -R reference.fasta

Function: Report putative somatic gene fusions from structural variants in a tumor-normal pair.

Usage: gemini fusions --min_qual 5 --in_cosmic_census tumor_normal.db

Function: Count the total number of covered loci

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

Function: Count the number of read events

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

Function: Count the number of ROD objects encountered along the reference

Usage: java -jar GenomeAnalysisTK.jar -T CountRODsByRef -R reference.fasta -o output.txt --rod input.vcf

Function: Generate a consensus sequence by applying variants from a VCF file to a reference genome, producing a personalized genomic sequence for a specific individual based on their genetic variants.

Usage: bcftools consensus [OPTIONS] <file.vcf.gz>

Supported input format: VCF, FASTA