| Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. |
hg clone https://toolshed.g2.bx.psu.edu/repos/lz_hust/gatktools
| Name | Version | Type | |
|---|---|---|---|
| ggplot2 | 0.9.3 | package | |
| picard | 1.56.0 | package | |
| samtools | 0.1.19 | package | |
| GATK2_PATH | set_environment | ||
| GATK2_SITE_OPTIONS | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| calculates covariates used to recalibrate base quality scores of reads | 2.8.0 | 16.01 | |
| on BAM files | 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 | |
| - perform local realignment | 2.8.1 | 16.01 | |
| on BAM files | 2.8.0 | 16.01 | |
| for use in local realignment | 2.8.1 | 16.01 | |
| in BAM files | 2.8.0 | 16.01 | |
| SNP and indel caller | 2.8.2 | 16.01 | |
| 2.8.0 | 16.01 | ||
| 2.8.1 | 16.01 | ||
| 2.8.0 | 16.01 | ||
| 2.8.1 | 16.01 | ||
| on VCF files | 2.8.0 | 16.01 | |
| 2.8.1 | 16.01 | ||
| from VCF files | 2.8.2 | 16.01 | |
| 2.8.0 | 16.01 | ||