Changes

   # This file contains information on how to process reference data sets.

   # This file contains information on how to process reference data sets.

   # dataset - name of data set, this label will be printed.

   # dataset - name of data set, this label will be printed.

   # type    - True Positives (TP) and False Positives (FP)

   # type    - True Positives (TP) and False Positives (FP).

   #          overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively

   #          overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively.

   #        - annotation

   #        - annotation.

   #          file is used for GENCODE annotation of frame shift and non frame shift Indels

   #          file is used for GENCODE annotation of frame shift and non frame shift Indels.

   # filter  - filter applied to variants for this particular data set

   # filter  - filter applied to variants for this particular data set.

   # path    - path of indexed BCF file

   # path    - path of indexed BCF file.

   #dataset             type         filter           path

   #dataset     type           filter                       path

   dbsnp                TP           INDEL           dbsnp.xxsnps_indels.sites.bcf

   1000g        TP             N_ALLELE==2&&VTYPE==INDEL   /net/fantasia/home/atks/ref/vt/grch37/1000G.snps_indels.sites.bcf

   mills                 TP           INDEL            mills.208620indels.sites.bcf

   mills       TP             N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/mills.208620indels.sites.bcf

   dbsnp        TP             N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/dbsnp.13147541variants.sites.bcf

  #mills.chip.common    TP          INDEL&&AF>0.005  grch37/mills.chip.158samples.8904indels.sites.bcf

   GENCODE_V19  cds_annotation  .                           /net/fantasia/home/atks/ref/vt/grch37/gencode.cds.bed.gz

   affy.exome.chip      TP           INDEL            affy.exome.chip.1249samples.316520variants.sites.bcf

   DUST        cplx_annotation .                           /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz

  #affy.exome.chip.poly  TP          INDEL&&AC!=0    grch37/affy.exome.chip.1249samples.316520variants.sites.bcf

 

   #affy.exome.chip.mono  FP          INDEL&&AC=0      grch37/affy.exome.chip.1249samples.316520variants.sites.bcf

   gencode.v19          annotation  .                gencode.v19.annotation.gtf.gz

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   usage : vt profile_indels [options] <in.vcf>

   usage : vt profile_indels [options] <in.vcf>