# This file contains information on how to process reference data sets.
# dataset - name of data set, this label will be printed.
# type    - True Positives (TP) and False Positives (FP).
#           overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively.
#         - annotation.
#           file is used for GENCODE annotation of frame shift and non frame shift Indels.
# filter  - filter applied to variants for this particular data set.
# path    - path of indexed BCF file.
#dataset     type              filter                       path
1000g        TP                N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/1000G.v5.snps.indels.complex.svs.sites.bcf
mills        TP                N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/mills.indels.sites.bcf
dbsnp        TP                N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/dbSNP138.snps.indels.complex.sites.bcf
gencode_v19  cds_annotation    .                            /net/fantasia/home/atks/ref/vt/grch37/gencode.v19.cds.bed.gz
dust         cplx_annotation   .                            /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz
rmsk         repeat_annotation .                            /net/fantasia/home/atks/ref/vt/grch37/rmsk.bed.gz