Galaxy Workflow ' bwa-gatk'

Annotation: Align with bwa and call SNPs/Indels with GATK

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: FASTQ Groomer
Output dataset 'output' from step 1
Illumina 1.3+
Show Advanced Options
Sanger (recommended)
ASCII
Do not Summarize Input (faster)
Step 4: FASTQ Groomer
Output dataset 'output' from step 2
Illumina 1.3+
Show Advanced Options
Sanger (recommended)
ASCII
Do not Summarize Input (faster)
Step 5: Map with BWA for Illumina
Use a built-in index
Populus_unmasked
Paired-end
Output dataset 'output_file' from step 3
Output dataset 'output_file' from step 4
Full Parameter List
0
0.04
1
-1
16
5
-1
2
3
11
4
False
False
3
10
500
100000
Yes
SciLife
ILLUMINA
False
Step 6: SAM-to-BAM
Locally cached
Output dataset 'output' from step 5
Step 7: flagstat
Output dataset 'output1' from step 6
Step 8: Realigner Target Creator
Locally cached
Output dataset 'output1' from step 6
None (value not yet validated)
select at runtime
Binding for reference-ordered datas
Basic
Basic
Step 9: Indel Realigner
Locally cached
Output dataset 'output1' from step 6
None (value not yet validated)
Output dataset 'output_interval' from step 8
select at runtime
Binding for reference-ordered datas
5.0
False
Basic
Basic
Step 10: Count Covariates
Locally cached
Output dataset 'output_bam' from step 9
(value not yet validated)
False
ReadGroupCovariate QualityScoreCovariate
select at runtime
Binding for reference-ordered datas
Basic
Basic
Step 11: Table Recalibration
Output dataset 'output_recal' from step 10
Locally cached
Output dataset 'output_bam' from step 9
None (value not yet validated)
Basic
Basic
Step 12: Unified Genotyper
Locally cached
Sample BAM files
Sample BAM file 1
Output dataset 'output_bam' from step 11
Populus_unmasked
select at runtime
Binding for reference-ordered datas
30.0
30.0
Basic
Basic