Repository revision
1:30e1dd77e99c

Repository 'table_recalibration'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration

Table Recalibration tool metadata
Miscellaneous
on BAM files
gatk_table_recalibration
toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table_recalibration/0.0.5
0.0.5
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table_recalibration/0.0.5 (this tool)
gatk_table_recalibration
Requirements (dependencies defined in the <requirements> tag set)
name version type
gatk 1.4 package
samtools 0.1.18 package
Functional tests
name inputs outputs required files
Test-1 gatk_param_type|gatk_param_type_selector: basic
reference_source|input_bam: gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam
reference_source|reference_source_selector: history
input_recal: gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv
analysis_param_type|analysis_param_type_selector: basic
reference_source|ref_file: phiX.fasta
output_bam: gatk_table_recalibration_out_1.bam
output_log: gatk_table_recalibration_out_1.log.contains
gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv
gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam
phiX.fasta
gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam
gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains