Galaxy Variant 101


StepAnnotation
Step 1: Input dataset
select at runtime
Child fq 1
Step 2: Input dataset
select at runtime
Child fq 2
Step 3: Input dataset
select at runtime
Mother fq 1
Step 4: Input dataset
select at runtime
Mother fq 2
Step 5: FastQC:Read QC
Output dataset 'output' from step 1
FastQC
select at runtime
Step 6: FastQC:Read QC
Output dataset 'output' from step 2
FastQC
select at runtime
Step 7: Map with BWA for Illumina
Use a built-in index
Homo_sapiens_nuHg19_mtrCRS
Paired-end
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Commonly Used
False
Use default job resource parameters
Step 8: Map with BWA for Illumina
Use a built-in index
Homo_sapiens_nuHg19_mtrCRS
Paired-end
Output dataset 'output' from step 3
Output dataset 'output' from step 4
Commonly Used
False
Use default job resource parameters
Step 9: Filter SAM
Output dataset 'output' from step 7
Flags
Flag 1
Read is paired
Yes
Flag 2
Read is mapped in a proper pair
Yes
Step 10: Filter SAM
Output dataset 'output' from step 8
Flags
Flag 1
Read is paired
Yes
Flag 2
Read is mapped in a proper pair
Yes
Step 11: SAM-to-BAM
Locally cached
Output dataset 'out_file1' from step 9
Use default job resource parameters
Step 12: SAM-to-BAM
Locally cached
Output dataset 'out_file1' from step 10
Use default job resource parameters
Step 13: Add or Replace Groups
Output dataset 'output1' from step 11
child
child
child
illumina
bc
Use pre-set defaults
True
Step 14: Add or Replace Groups
Output dataset 'output1' from step 12
mother
mother
mother
illumina
bc
Use pre-set defaults
True
Step 15: Merge BAM Files
child-mother
True
Output dataset 'outFile' from step 13
Output dataset 'outFile' from step 14
Input Files
Step 16: Naive Variant Caller
Locally cached
BAM files
BAM file 1
Output dataset 'output1' from step 15
Homo_sapiens_nuHg19_mtrCRS
Restrict to regions
10
20
Not available.
1
True
True
Show Advanced Options
uint8
False
Step 17: FreeBayes
Locally cached
Sample BAM files
Sample BAM file 1
Output dataset 'output1' from step 15
Homo_sapiens_nuHg19_mtrCRS
Advanced
False
False
Limit to region
chrM
1000
10000
select at runtime
select at runtime
select at runtime
Do not provide
select at runtime
Do not set
Do not set
Do not include
Do not set
False
Do not set
Do not set
Do not set
Do not set
Use default job resource parameters
Step 18: Variant Annotator
Output dataset 'output_vcf' from step 16
1.0
10
False
True
True
Step 19: Filter
Output dataset 'output' from step 18
c16 >= 0.02
1