VEP_filter.R

Variant prioritization algorithm developed by Nutchavadee Vorasan for SUDS project to filter variants annotated with VEP by R

VEP annotation was performed using GRCh37 (hg19) annotation

VEP_filter.Chunky.template.R

Editor: K2

Synopsis: Read file in chunks (for Large file size)

Support: VEP95.2 , dbSNP 3.5a

Oncotator_filter.R

Editor: K2

Synopsis: for filtering results from Oncotator Filtering default:

1. Select variants with 'PASS'

2. Filter with Impact (High, Moderate)

3. Filter with LR and SVM (include "D" or "-")

4. Filter with CADD score (exculde values which is "< 15")

5. Filter with Allele Frequency (Using General AF to exclude variant that greater than 10% (>0.1) )

• able to adjust filtering steps

Support: Oncotator1.9.8.0+