| The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. http://www.broadinstitute.org/gatk/about/ |
hg clone https://testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/gatk2
| Repository package_samtools_0_1_19 revision a0ab0fae27e5 owned by iuc |
| Repository package_picard_1_56_0 revision 7206dbf34dcd owned by devteam |
| Name | Version | Type | |
|---|---|---|---|
| picard | 1.56.0 | package | |
| samtools | 0.1.19 | package | |
| GATK2_PATH | set_environment | ||
| GATK2_SITE_OPTIONS | set_environment | ||
| GATK2_JAVA_OPTIONS | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| 2.8.0 | 16.01 | ||
| 2.8.0 | 16.01 | ||
| 2.8.1 | 16.01 | ||
| in BAM files | 2.8.0 | 16.01 | |
| calculates covariates used to recalibrate base quality scores of reads | 2.8.0 | 16.01 | |
| on BAM files | 2.8.0 | 16.01 | |
| on BAM files | 2.8.0 | 16.01 | |
| 2.8.1 | 16.01 | ||
| SNP and indel caller | 2.8.1 | 16.01 | |
| 2.8.1 | 16.01 | ||
| on VCF files | 2.8.0 | 16.01 | |
| 2.8.0 | 16.01 | ||
| for use in local realignment | 2.8.1 | 16.01 | |
| Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region | 2.8.2 | 16.01 | |
| from VCF files | 2.8.1 | 16.01 | |
| - perform local realignment | 2.8.1 | 16.01 | |