# This file contains information on how to process reference data sets.
#
# dataset - name of data set, this label will be printed.
# type    - Truth set (Truth) and False set (False)
#           overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively
#         - cds_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
# 
# Please do not change order of data set.  profile_na12878 assumes this order.
#
#dataset                    type              filter                                        path
broad.kb                    BroadKB           VTYPE==INDEL&&N_ALLELE==2                     /net/fantasia/home/atks/ref/vt/grch37/NA12878.broad.kb.snps.indels.complex.genotypes.bcf
broad.kb.nondust            BroadKB           VTYPE==INDEL&&N_ALLELE==2&&~INFO.DUST         /net/fantasia/home/atks/ref/vt/grch37/NA12878.broad.kb.snps.indels.complex.genotypes.bcf
broad.kb.dust               BroadKB           VTYPE==INDEL&&N_ALLELE==2&&INFO.DUST          /net/fantasia/home/atks/ref/vt/grch37/NA12878.broad.kb.snps.indels.complex.genotypes.bcf
illumina.platinum           Truth             PASS&&VTYPE==INDEL&&N_ALLELE==2               /net/fantasia/home/atks/ref/vt/grch37/NA12878.illumina.platinum.snps.indels.complex.genotypes.bcf
illumina.platinum.nondust   Truth             PASS&&VTYPE==INDEL&&N_ALLELE==2&&~INFO.DUST   /net/fantasia/home/atks/ref/vt/grch37/NA12878.illumina.platinum.snps.indels.complex.genotypes.bcf
illumina.platinum.dust      Truth             PASS&&VTYPE==INDEL&&N_ALLELE==2&&INFO.DUST    /net/fantasia/home/atks/ref/vt/grch37/NA12878.illumina.platinum.snps.indels.complex.genotypes.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