version: 13

aliases:
  human: true
  snpeff: hg19
  ensembl: homo_sapiens

variation:
  dbsnp: ../variation/dbsnp_138.vcf.gz
  train_hapmap: ../variation/hapmap_3.3.vcf.gz
  train_omni: ../variation/1000G_omni2.5.vcf.gz
  train_1000g: ../variation/1000G_phase1.snps.high_confidence.vcf.gz
  train_indels: ../variation/Mills_and_1000G_gold_standard.indels.vcf.gz
  cosmic: ../variation/cosmic-v68-hg19.vcf.gz
  lcr: ../variation/LCR.bed.gz
  sv_repeat: ../variation/sv_repeat_telomere_centromere.bed
  dbnsfp: ../variation/dbNSFP_v2.6.gz
  ancestral: ../variation/human_ancestor.fa.rz

rnaseq:
  transcripts: ../rnaseq/ref-transcripts.gtf
  transcripts_mask: ../rnaseq/ref-transcripts-mask.gtf
  transcriptome_index:
    tophat: ../rnaseq/tophat/hg19_transcriptome.ver

version: 14

aliases:
  human: true
  snpeff: hg19
  ensembl: homo_sapiens

variation:
  dbsnp: ../variation/dbsnp_138.vcf.gz
  train_hapmap: ../variation/hapmap_3.3.vcf.gz
  train_omni: ../variation/1000G_omni2.5.vcf.gz
  train_1000g: ../variation/1000G_phase1.snps.high_confidence.vcf.gz
  train_indels: ../variation/Mills_and_1000G_gold_standard.indels.vcf.gz
  cosmic: ../variation/cosmic-v68-hg19.vcf.gz
  lcr: ../variation/LCR.bed.gz
  sv_repeat: ../variation/sv_repeat_telomere_centromere.bed
  dbnsfp: ../variation/dbNSFP_v2.6.gz
  ancestral: ../variation/human_ancestor.fa.rz

rnaseq:
  transcripts: ../rnaseq/ref-transcripts.gtf
  transcripts_mask: ../rnaseq/ref-transcripts-mask.gtf
  transcriptome_index:
    tophat: ../rnaseq/tophat/hg19_transcriptome.ver
  dexseq: ../rnaseq/ref-transcripts.dexseq.gff3
  refflat: ../rnaseq/ref-transcripts.refFlat
  rRNA_fa: ../rnaseq/rRNA.fa

Add extra RNA-seq annotation files to hg19 resources.
Add extra RNA-seq annotation files to hg19 resources.
