neglisible change due to change in running argument
change in VEP annotation report: report only coding genes in REFSEQ
minor change: executing command line changed
minor change: running command change
change to insert (not replace) data into 'mutation' table
change to insert (not replace) data into 'mutation_rsq' table
changes in 'mutation_normal' table:
- table schema changed : size of certain fields were changed
- 'cosmic' table is left joined later.
change to insert (not replace) data into 'splice_eiJunc' table
change to insert (not replace) data into 'splice_normal' table
change to insert (not replace) data into 'splice_skip' table
change in parsing sample id (due to snu samples (S**[ABC])
change due to running different command line
change to accommodate individuals with multiple recurrent samples.
Change which fields from VEP annotation is printed and how they are handled
- regulatiory (general) & TFBS : regulatory_region_variants / TF_binding_site_variant
- splicing site / UTR
- coding exons
- non-coding transcripts or introns are not reported
Skips when gzipped file (.pileup.gz) is found.
Simplifies command line.
Minor change due to executing command change
Change in mutation effect description (due to terms from VEP)
minor change
Change in mutation descriptions entered into DB