CI-Intronic-Variant

From vcf file, we get 5 columns of informations.

Chr - Pos - Ref - Var - strand

This script is to locate any intronic variant which may cause potential splice site change.

1. get a sequence from reference; use the nucleotide position (+/- 30) (len = 61)
2. If strand == '-'; reverse the sequence
3. Change the Ref to Var in seq No.30 (len-1)/2
4. Get the sequence 30 +/- 5 to do a sliding window (bin size = 2) check for possible AG/GT if AG exist, get the before 20 (+AG) base and after 3 base; count for MaxEnt3 if GT exist, get the before 3 base and after 6 (+AG) base; count for MaxEnt5 if MaxEntScore > threshold (5?); count for Ref_MaxEntScore if difference > threshold (3?) get the sequence, use the nucleotide position (+/- 500) AG backward search 500bp for GT (sliding window size = 2) GT forward search 500bp for AG (sliding window size = 2) if match, MaxEnt Score it check for threshold print the list