| java -jar GenomeAnalysisTK.jar |
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 |
Create plots to visualize base recalibration results |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ReadGroupProperties -R reference.fasta -I example1.bam -I example2.bam -o readgroup_report.grp |
Collect statistics about read groups and their properties |
| java -jar GenomeAnalysisTK.jar |
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] |
Call SNPs and indels on a per-locus basis |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ValidateVariants -R reference.fasta -V input.vcf --validationTypeToExclude ALLELES |
Validate a VCF file with an extra strict set of criteria |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T ReadLengthDistribution -R reference.fasta -I example.bam -o example.tbl |
Collect read length statistics |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -R reference.fasta -T CountReads -I input.bam [-L input.intervals] |
Count the number of reads |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T Pileup -R reference.fasta -I my_reads.bam -L chr1:257-267 -o output.txt |
Print read alignments in Pileup-style format |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V input.vcf -o output.vcf -sn SAMPLE_1_PARC -sn SAMPLE_1_ACTG -se 'SAMPLE.+PARC' |
Select a subset of variants from a larger callset |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T RandomlySplitVariants -R reference.fasta -V input.vcf -o1 output_1.vcf -o2 output_2.vcf |
Randomly split variants into different sets |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T QCRef -R reference.fasta |
Quality control for the reference fasta |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountReadEvents -R reference.fasta -I input.bam -o output.grp [-L input.intervals] |
Count the number of read events |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountLoci -R reference.fasta -I input.bam -o output.txt [-L input.intervals] |
Count the total number of covered loci |
| java -jar GenomeAnalysisTK.jar |
java -jar GenomeAnalysisTK.jar -T CountRODsByRef -R reference.fasta -o output.txt --rod input.vcf |
Count the number of ROD objects encountered along the reference |
| GEMINI fusions |
gemini fusions --min_qual 5 --in_cosmic_census tumor_normal.db |
Report putative somatic gene fusions from structural variants in a tumor-normal pair. |