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version: 47
aliases:
human: true
snpeff: GRCh38.99
ensembl: homo_sapiens_merged_vep_100_GRCh38
variation:
dbsnp: ../variation/dbsnp.vcf.gz
dbnsfp: ../variation/dbNSFP.txt.gz
dbscsnv: ../variation/dbscSNV.txt.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.vcf.gz
clinvar: ../variation/clinvar.vcf.gz
esp: ../variation/esp.vcf.gz
exac: ../variation/exac.vcf.gz
gnomad_exome: ../variation/gnomad_exome.vcf.gz
gnomad_genome: ../variation/gnomad_genome.vcf.gz
lcr: ../coverage/problem_regions/repeats/LCR.bed.gz
polyx: ../coverage/problem_regions/repeats/polyx.bed.gz
gc_profile: ../coverage/gc/GC_profile.1000bp.cnp
germline_het_pon: ../variation/germline_het_pon.bed.gz
sv_repeat: ../coverage/problem_regions/repeats/sv_repeat_telomere_centromere.bed
qsignature: ../variation/qsignature.txt
genesplicer: ../variation/genesplicer
editing: ../editing/RADAR.bed.gz
genotype2phenotype: ../variation/G2P.csv
af_only_gnomad: ../variation/af_only_gnomad.vcf.gz
purecn_mappability: ../coverage/mappability/GCA_000001405.15_GRCh38_no_alt_analysis_set_100.bw
simple_repeat: ../coverage/problem_regions/repeats/simple_repeat.bed
rnaseq:
transcripts: ../rnaseq/ref-transcripts.gtf
transcripts_mask: ../rnaseq/ref-transcripts-mask.gtf
transcriptome_index:
tophat: ../rnaseq/tophat/hg38_transcriptome.ver
dexseq: ../rnaseq/ref-transcripts.dexseq.gff3
refflat: ../rnaseq/ref-transcripts.refFlat
rRNA_fa: ../rnaseq/rRNA.fa
srnaseq:
srna_transcripts: ../srnaseq/srna-transcripts.gtf
mirbase_hairpin: ../srnaseq/hairpin.fa
mirbase_mature: ../srnaseq/mature.fa
mirdeep2_fasta: ../srnaseq/Rfam_for_miRDeep.fa
trna_fasta: ../srnaseq/trna_mature_pre.fa
mint_lookup: ../srnaseq/LookupTable.tRFs.MINTmap_v1.txt
mint_space: ../srnaseq/tRNAspace.Spliced.Sequences.MINTmap_v1.fa
mint_other: ../srnaseq/OtherAnnotations.MINTmap_v1.txt