Workflow_trio variant calling_final project


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Input dataset
select at runtime
Step 5: Input dataset
select at runtime
Step 6: Input dataset
select at runtime
Step 7: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
Step 8: FASTQ Groomer
Output dataset 'output' from step 1
Sanger & Illumina 1.8+
Hide Advanced Options
Step 9: FastQC
Output dataset 'output' from step 2
select at runtime
select at runtime
Step 10: FASTQ Groomer
Output dataset 'output' from step 2
Sanger & Illumina 1.8+
Hide Advanced Options
Step 11: FastQC
Output dataset 'output' from step 3
select at runtime
select at runtime
Step 12: FASTQ Groomer
Output dataset 'output' from step 3
Sanger & Illumina 1.8+
Hide Advanced Options
Step 13: FastQC
Output dataset 'output' from step 4
select at runtime
select at runtime
Step 14: FASTQ Groomer
Output dataset 'output' from step 4
Sanger & Illumina 1.8+
Hide Advanced Options
Step 15: FastQC
Output dataset 'output' from step 5
select at runtime
select at runtime
Step 16: FASTQ Groomer
Output dataset 'output' from step 5
Sanger & Illumina 1.8+
Hide Advanced Options
Step 17: FastQC
Output dataset 'output' from step 6
select at runtime
select at runtime
Step 18: FASTQ Groomer
Output dataset 'output' from step 6
Sanger & Illumina 1.8+
Hide Advanced Options
Step 19: Trimmomatic
Paired-end (two separate input files)
Output dataset 'output_file' from step 8
Output dataset 'output_file' from step 10
False
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the end of a read, if below a threshold quality (TRAILING)
30
Step 20: Trimmomatic
Paired-end (two separate input files)
Output dataset 'output_file' from step 12
Output dataset 'output_file' from step 14
False
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the end of a read, if below a threshold quality (TRAILING)
30
Step 21: Trimmomatic
Paired-end (two separate input files)
Output dataset 'output_file' from step 16
Output dataset 'output_file' from step 18
False
Trimmomatic Operations
Trimmomatic Operation 1
Cut bases off the end of a read, if below a threshold quality (TRAILING)
30
Step 22: Bowtie2
Paired-end
Output dataset 'fastq_out_r1_paired' from step 19
Output dataset 'fastq_out_r2_paired' from step 19
False
False
No
Use a built-in genome index
hg19
Do not set
1: Default setting only
No, just use defaults
False
Use default job resource parameters
Step 23: Bowtie2
Paired-end
Output dataset 'fastq_out_r1_paired' from step 20
Output dataset 'fastq_out_r2_paired' from step 20
False
False
No
Use a built-in genome index
hg19
Do not set
1: Default setting only
No, just use defaults
False
Use default job resource parameters
Step 24: Bowtie2
Paired-end
Output dataset 'fastq_out_r1_paired' from step 21
Output dataset 'fastq_out_r2_paired' from step 21
False
False
No
Use a built-in genome index
hg19
Do not set
1: Default setting only
No, just use defaults
False
Use default job resource parameters
Step 25: AddOrReplaceReadGroups
Output dataset 'output' from step 22
False
01
False
Father
False
A
ILLUMINA
1
Empty.
Empty.
Not available.
Empty.
Lenient
Step 26: AddOrReplaceReadGroups
Output dataset 'output' from step 23
False
02
False
Mother
False
B
ILLUMINA
2
Empty.
Empty.
Not available.
Empty.
Lenient
Step 27: AddOrReplaceReadGroups
Output dataset 'output' from step 24
False
03
False
Child
False
C
ILLUMINA
3
Empty.
Empty.
Not available.
Empty.
Lenient
Step 28: FreeBayes
Locally cached
Output dataset 'outFile' from step 27,Output dataset 'outFile' from step 26,Output dataset 'outFile' from step 25
hg19
Do not limit
2. Simple diploid calling with filtering and coverage
0
Use default job resource parameters
Step 29: VCFfilter:
Output dataset 'output_vcf' from step 28
more filters
False

No value found for 'Filter entire records, not just alleles'. Using default: 'False'.

False

No value found for 'Tag vcf records as positively filtered with this tag, print all records'. Using default: 'False'.

False

No value found for 'Tag vcf records as negatively filtered with this tag, print all records'. Using default: 'False'.

False

No value found for 'Append the existing filter tag, don't just replace it'. Using default: 'False'.

False

No value found for 'Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag'. Using default: 'False'.

False

No value found for 'Inverts the filter, e.g. grep -v'. Using default: 'False'.

False

No value found for 'Use logical OR instead of AND to combine filters'. Using default: 'False'.

Not available.

No value found for 'Specify a region on which to target the filtering'.

Step 30: SnpEff eff:
Output dataset 'out_file1' from step 29
VCF
VCF (only if input is VCF)
False

No value found for 'Create CSV report, useful for downstream analysis (-csvStats)'. Using default: 'False'.

Locally installed snpEff database
GRCh37.74
Regulation options:
None
5000 bases
2 bases
Use Defaults
Nothing selected.
select at runtime
select at runtime
Nothing selected.
No
Use default (based on input type)
Empty.
True
True
Step 31: ANNOVAR Annotate VCF
Output dataset 'snpeff_output' from step 30
refGene gencodeV19
None
None
Tabular
Step 32: Group
Output dataset 'output' from step 31
11
False
Nothing selected.
Operations
Operation 1
Count
1
NO
Not available.
Step 33: Group
Output dataset 'output' from step 31
2
False
Nothing selected.
Operations
Operation 1
Count
2
NO
Not available.
Step 34: Sort
Output dataset 'out_file1' from step 32
2
Numerical sort
Descending order
Column selections
0

No value found for 'Number of header lines to skip'. Using default: '0'.

Step 35: Sort
Output dataset 'out_file1' from step 33
2
Numerical sort
Descending order
Column selections
0

No value found for 'Number of header lines to skip'. Using default: '0'.