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://toolshed.g2.bx.psu.edu/repos/iuc/gatk2
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 |
---|---|---|---|
on BAM files | 2.8.0 | any | |
in BAM files | 2.8.0 | any | |
on BAM files | 2.8.0 | any | |
2.8.0 | any | ||
2.8.0 | any | ||
calculates covariates used to recalibrate base quality scores of reads | 2.8.0 | any | |
2.8.0 | any | ||
for use in local realignment | 2.8.0 | any | |
SNP and indel caller | 2.8.0 | any | |
2.8.0 | any | ||
on VCF files | 2.8.0 | any | |
from VCF files | 2.8.0 | any | |
- perform local realignment | 2.8.0 | any | |
2.8.0 | any | ||
Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region | 2.8.0 | any | |
2.8.0 | any |