Published Workflows | curtish | SOP: VCF snpEffect and index with sample name

Galaxy Workflow ' SOP: VCF snpEffect and index with sample name'


StepAnnotation
Step 1: Input dataset
select at runtime
VCF input
Step 2: Create single interval
chrLAB
0
0
${sample_name_no_spaces}
plus
Step 3: Unknown Tool with id 'snpEff'
Step 4: Add column
.
Output dataset 'out_file1' from step 2
NO
Step 5: Compute
c8.split("EFF=").pop().split(";").pop(0)
Output dataset 'output' from step 3
NO
extract snpEff EFFECT
Step 6: Cut
c1,c2,c7,c1,c4,c2,c7,c4,c4,c4,c4,c4
Tab
Output dataset 'out_file1' from step 4
Step 7: Compute
str(c10.pop(0))+str(c10.pop(0))+str(c10.pop(0))
Output dataset 'out_file1' from step 5
NO
extract snpEff het/hom call
Step 8: Concatenate datasets
Output dataset 'out_file1' from step 6
Datasets
Dataset 1
Output dataset 'out_file1' from step 7
Step 9: Compute
str(c1)+':'+str(int(c2))+':'+str(c4)
Output dataset 'out_file1' from step 8
NO
add idx3=index(chr:pos:ref)
Step 10: Compute
str(c1)+':'+str(int(c2))+':'+str(c4)+':'+str(c5)
Output dataset 'out_file1' from step 9
NO
add idx4=index(chr:pos:ref:alt)
Step 11: Cut
c13
Tab
Output dataset 'out_file1' from step 10
extract idxRef
Step 12: Cut
c14
Tab
Output dataset 'out_file1' from step 10
extract idxAlt
Step 13: Cut
c13,c5,c6,c12,c11
Tab
Output dataset 'out_file1' from step 10
idxRef plus other column {alt,qual,het,eff}