Published Workflows | curtish | SOP: VCF_fullidx remove common SNPs

Galaxy Workflow ' SOP: VCF_fullidx remove common SNPs'


StepAnnotation
Step 1: Input dataset
select at runtime
VCF_fullidx: VCF from snpEffects with 3 extra index columns (c12=het/hom,c13=idxRef,c14=idxAlt)
Step 2: Input dataset
select at runtime
tabular file with idxAlt (chr:pos:ref:alt) of common SNPs to remove in c1
Step 3: Compare two Datasets
Output dataset 'output' from step 1
14
Output dataset 'output' from step 2
1
Non Matching rows of 1st dataset
Step 4: Cut
c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11
Tab
Output dataset 'out_file1' from step 3
Trim VCF_fullidx back down to a VCF