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view annovar_yaml/YAML_annovar.yml @ 13:aeb0873c9218 draft

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author niels
date Tue, 14 May 2019 07:19:12 -0400
parents 856448f167da
children 7f4fb56714e8
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GENERAL:
  - APPLICATION: 'annovar'
    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
    CODING_ANNOVAR: 'coding_annovar.pl'
    TABLE_ANNOVAR: 'table_annovar.pl'
    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
    DOT2UNDERLINE: 'yes'
    NASTRING: '.'
    OTHERINFO: 'yes'
    POLISH: 'yes'
    REMOVE: 'yes'
    THREAD: '8'
    INPUTFORMAT: 'vcfinput'
    SPECIES: 'human'
    BUILD: 'hg19'
ANALYSIS:
  DATABASES:
  - NAME: 'cosmic84'
    PROTOCOL: 'cosmic'
    VERSION: '84'
    COMMENT: '20190221'
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    OPERATION: 'f' 
    COLSWANTED: '4'
  - NAME: 'refgene19'
    PROTOCOL: 'refgene'
    VERSION: '19' 
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    COMMENT: '20190210'
    OPERATION: 'g'
    HGVS: 'yes'
    SPLICING: '6'
    EXONSPLIC: 'yes'
  - NAME: 'ncbiRefSeq_UMCU'
    PROTOCOL: 'ncbiRefSeq'
    VERSION: '_UMCU'
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    COMMENT: "100519"
    OPERATION: 'g'
    HGVS: 'yes'
    SPLICING: '6'
    EXONSPLIC: 'yes'
  - NAME: 'avsnp150'
    PROTOCOL: 'avsnp'
    VERSION: '150'
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    OPERATION: 'f'
    COLSWANTED: '1'
  - NAME: 'clinvar_20180603'
    PROTOCOL: 'clinvar'
    VERSION: '_20180603'
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    OPERATION: 'f'
    COLSWANTED: '5'
  - NAME: 'class100519'
    PROTOCOL: 'class'
    VERSION: '100519'
    AVAILABLE: 'yes'
    REQUIRED: 'yes'
    OPERATION: 'f'
    COLSWANTED: '1'