Download Biofilter - 2.2 User Manual

--gene-file / GENE_FILE....................................................................................................................................................................... 19
--gene-identifier-type / GENE_IDENTIFIER_TYPE ................................................................................................................. 19
--allow-ambiguous-genes / ALLOW_AMBIGUOUS_GENES ................................................................................................. 20
--gene-search / GENE_SEARCH........................................................................................................................................................ 20
--group / GROUP ..................................................................................................................................................................................... 20
--group-file / GROUP_FILE ................................................................................................................................................................. 20
--group-identifier-type / GROUP_IDENTIFIER_TYPE............................................................................................................ 20
--allow-ambiguous-groups / ALLOW_AMBIGUOUS_GROUPS ............................................................................................ 20
--group-search / GROUP_SEARCH .................................................................................................................................................. 20
--source / SOURCE ................................................................................................................................................................................. 20
--source-file / SOURCE_FILE ............................................................................................................................................................. 20
Alternate Input Data Options ........................................................................................................................................................ 21
--alt-snp / ALT_SNP ............................................................................................................................................................................... 21
--alt-snp-file / ALT_SNP_FILE ........................................................................................................................................................... 21
--alt-position / ALT_POSITION ......................................................................................................................................................... 21
--alt-position-file / ALT_POSITION_FILE ..................................................................................................................................... 21
--alt-region / ALT_REGION................................................................................................................................................................. 21
--alt-region-file / ALT_REGION_FILE ............................................................................................................................................. 21
--alt-gene / ALT_GENE ......................................................................................................................................................................... 21
--alt-gene-file / ALT_GENE_FILE ..................................................................................................................................................... 21
--alt-gene-search / ALT_GENE_SEARCH ...................................................................................................................................... 22
--alt-group / ALT_GROUP.................................................................................................................................................................... 22
--alt-group-file / ALT_GROUP_FILE................................................................................................................................................ 22
--alt-group-search / ALT_GROUP_SEARCH ................................................................................................................................. 22
--alt-source / ALT_SOURCE ................................................................................................................................................................ 22
--alt-source-file / ALT_SOURCE_FILE ............................................................................................................................................ 22
Positional Matching Options .......................................................................................................................................................... 22
--region-position-margin / REGION_POSITION_MARGIN ................................................................................................... 22
--region-match-percent / REGION_MATCH_PERCENT ......................................................................................................... 22
--region-match-bases / REGION_MATCH_BASES..................................................................................................................... 23
Model Building Options ................................................................................................................................................................... 23
--maximum-model-count / MAXIMUM_MODEL_COUNT ..................................................................................................... 23
--alternate-model-filtering / ALTERNATE_MODEL_FILTERING ....................................................................................... 23
--all-pairwise-models / ALL_PAIRWISE_MODELS ................................................................................................................... 23
--maximum-model-group-size / MAXIMUM_MODEL_GROUP_SIZE ................................................................................ 23
--minimum-model-score / MINIMUM_MODEL_SCORE ......................................................................................................... 23
--sort-models / SORT_MODELS ........................................................................................................................................................ 23
Output Options .................................................................................................................................................................................... 24
--quiet / QUIET ........................................................................................................................................................................................ 24
--verbose / VERBOSE ............................................................................................................................................................................ 24
--prefix / PREFIX ..................................................................................................................................................................................... 24
--overwrite / OVERWRITE ................................................................................................................................................................. 24
--stdout / STDOUT ................................................................................................................................................................................. 24
--report-invalid-input / REPORT_INVALID_INPUT................................................................................................................. 24
--filter / FILTER ....................................................................................................................................................................................... 24
--annotate / ANNOTATE...................................................................................................................................................................... 24
--model / MODEL.................................................................................................................................................................................... 24
Input File Formats ......................................................................................................................... 25
Configuration Files............................................................................................................................................................................. 25
SNP List Input Files............................................................................................................................................................................ 26
Position Data Input Files ................................................................................................................................................................. 26
Region Data Input Files .................................................................................................................................................................... 27
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