Accessible Workflow | TP53 mutation screening and filtering

Galaxy Workflow ' TP53 mutation screening and filtering'

Annotation: TP53 Mutation analysis from MinION sequencing. Change attributes of input files before starting. Fastq file has to be loaded as Fastqsanger and hg19 genome database has to be specified. In IARC TP53 dataset hg19 genome database has to be specified.

StepAnnotation
Step 1: BWA-MEM
Local cache
hg19
Single
select at runtime
Do not set
3.Full list of options
Set
14
20
100
10.0
20
500
0.5
0
50
False
False
False
Set
1
1
1
1
0
17
Do not set
Use default job resource parameters
Input file has to be fastqsanger and hg19 has to be specified in their attributes.
Step 2: Input dataset
select at runtime
Specify hg19 database in their attributes after loading and before starting the workflow.
Step 3: BamLeftAlign
Locally cached
Output dataset 'bam_output' from step 1
hg19
5
Step 4: Generate pileup
Use a built-in index
Output dataset 'output_bam' from step 3
hg19
Not available.
Not available.
Not available.
No
Step 5: Varscan
Output dataset 'output1' from step 4
single nucleotide variation
50
10
5
0.01
0.75
0.05
yes
Empty.
Step 6: Varscan
Output dataset 'output1' from step 4
insertions and deletions
50
13
10
0.01
0.75
0.05
yes
Empty.
Step 7: VCFtoTab-delimited:
Output dataset 'output' from step 5
True
Nothing
Step 8: VCFtoTab-delimited:
Output dataset 'output' from step 6
True
Nothing
Step 9: Join two Datasets
Output dataset 'output' from step 2
2
Output dataset 'out_file1' from step 7
2
No
No
No
No

No value found for 'Keep the header lines'. Using default: ''.

Be sure that hg19 is specified in "IARC TP53 dataset v.R17 reformatted"
Step 10: Compute
len(c4)-len(c5)
Output dataset 'out_file1' from step 8
NO
Step 11: Filter
Output dataset 'out_file1' from step 9
c11==c54 and c12==c55
1
Step 12: Join two Datasets
Output dataset 'output' from step 2
2
Output dataset 'out_file1' from step 10
2
No
No
No
No

No value found for 'Keep the header lines'. Using default: ''.

Be sure that hg19 is specified in "IARC TP53 dataset v.R17 reformatted"
Step 13: Cut
c1, c2, c11, c12, c54, c55, c69, c3, c4, c5, c6, c7, c8, c9, c10, c14, c16, c18, c20, c22, c24, c26, c28, c30, c32, c34, c36, c38, c40, c42, c44, c46, c48, c50
Tab
Output dataset 'out_file1' from step 11
Step 14: Filter
Output dataset 'out_file1' from step 12
c14=='ins' or c14=='del'
0
Step 15: Select first
1
Output dataset 'out_file1' from step 13
Step 16: Trim
Output dataset 'out_file1' from step 14
11
4
0
No
Nothing selected.
Step 17: Filter
Output dataset 'out_file1' from step 16
((c14=='del' and c78>0) or (c14=='ins' and c78<0)) and c11==abs(c78)
0
Step 18: Cut
c1, c2, c11, c12, c54, c55, c69, c3, c4, c5, c6, c7, c8, c9, c10, c14, c16, c18, c20, c22, c24, c26, c28, c30, c32, c34, c36, c38, c40, c42, c44, c46, c48, c50
Tab
Output dataset 'out_file1' from step 17
Step 19: Concatenate datasets
Output dataset 'out_file1' from step 15
Datasets
Dataset 1
Output dataset 'out_file1' from step 18