refdocs_tree.txt

my_mc3
|-- mc3
#------Directory tree removed for brevity----------------
`-- ref
    |-- 1000G_phase1.indels.hg19.sites.vcf
    |-- 1000G_phase1.indels.hg19.sites.vcf.idx
    |-- b37_cosmic_v54_120711.vcf.gz
    |-- b37_cosmic_v54_120711.vcf.gz.tbi
    |-- centromere_hg19.bed
    |-- dbsnp_132_b37.leftAligned.vcf.gz
    |-- dbsnp_132_b37.leftAligned.vcf.gz.tbi
    |-- gaf_20111020+broad_wex_1.1_hg19.bed
    |-- gencode.v19.basic.exome.bed
    |-- gencode.v19.basic.exome.bed.idx
    |-- Homo_sapiens_assembly19.dict
    |-- Homo_sapiens_assembly19.dict.gz
    |-- Homo_sapiens_assembly19.fasta
    |-- Homo_sapiens_assembly19.fasta.fai
    |-- Homo_sapiens_assembly19.fasta.gz
    |-- Homo_sapiens_assembly19.fasta.gz.fai
    |-- Homo_sapiens_assembly19.fasta.gz.gzi
    |-- markfiles
    |   |-- mark_samples
    |   |   |-- contestkeys.txt
    |   |   |-- mark_bitgt.txt
    |   |   |-- mark_nonexonic.txt
    |   |   |-- pancan.merged.v0.2.exac_pon_tagged.txt
    |   |   |-- pancan.merged.v0.2.pfiltered.broad_pon_tagged_v2.txt
    |   |   |-- pcadontusekeys.txt
    |   |   `-- strandBias.filter_v2.txt
    |   `-- mark_variants
    |       |-- ndp.mark.txt
    |       |-- nonpreferredpair_maf_keys.txt
    |       |-- oxog.annotation
    |       `-- wga_maf_keys.txt
    |-- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
    |-- Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx
    |-- oxog_filter
    |   |-- ref_data_for_oxog_all_permissions.tar.gz
    |   `-- ref_data_for_oxog.tar
    `-- vep
        |-- ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz
        |-- ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz.tbi
        `-- homo_sapiens
            |-- 86_GRCh37
            |   |-- 1
            |   |   |-- 100000001-101000000.gz
            |   |   |-- 100000001-101000000_reg.gz
            |   |   |-- 100000001-101000000_var.gz
            |   |   |-- 10000001-11000000.gz
            |   |   |-- 10000001-11000000_reg.gz
            |   |   |-- 10000001-11000000_var.gz
 
#------Portion of tree removed for brevity----------------
 
            |       |-- 8000001-9000000.gz
            |       |-- 8000001-9000000_reg.gz
            |       |-- 8000001-9000000_var.gz
            |       |-- 9000001-10000000.gz
            |       |-- 9000001-10000000_reg.gz
            |       `-- 9000001-10000000_var.gz
            |-- Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
            |-- Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz.fai
            `-- Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz.gzi