.. contents:: Quick navigation :depth: 2 Main Pipeline - ``genipe-launcher`` ==================================== Execute the genome-wide imputation pipeline. General options ---------------- .. table:: +-----------------------+-------------------------------------------------+ | Option | Description | +=======================+=================================================+ | ``-h``, ``--help`` | Show this help message and exit. | +-----------------------+-------------------------------------------------+ | ``-v``, ``--version`` | Show program's version number and exit. | +-----------------------+-------------------------------------------------+ | ``--debug`` | Set the logging level to debug. | +-----------------------+-------------------------------------------------+ | ``--thread THREAD`` | Number of threads [``1``]. | +-----------------------+-------------------------------------------------+ Input options -------------- .. table:: +----------------------+--------------------------------------------------+ | Option | Description | +======================+==================================================+ | ``--bfile PREFIX`` | The prefix of the binary pedfiles (input data). | +----------------------+--------------------------------------------------+ | ``--reference FILE`` | The human reference to perform an initial strand | | | check (useful for genotyped markers not in the | | | IMPUTE2 reference files) (optional). | +----------------------+--------------------------------------------------+ Output options --------------- .. table:: +-------------------------------+-----------------------------------------+ | Option | Description | +===============================+=========================================+ | ``--chrom CHROM [CHROM ...]`` | The chromosomes to process. It is | | | possible to write 'autosomes' to process| | | all the autosomes (from chromosome 1 to | | | 22, inclusively). | +-------------------------------+-----------------------------------------+ | ``--output-dir DIR`` | The name of the output directory. | | | [``genipe``] | +-------------------------------+-----------------------------------------+ | ``--bgzip`` | Use bgzip to compress the impute2 files.| +-------------------------------+-----------------------------------------+ HPC options ------------ .. table:: +-------------------------+-----------------------------------------------+ | Option | Description | +=========================+===============================================+ | ``--use-drmaa`` | Launch tasks using DRMAA. | +-------------------------+-----------------------------------------------+ | ``--drmaa-config FILE`` | The configuration file for tasks (use this | | | option when launching tasks using DRMAA). This| | | file should describe the walltime and the | | | number of nodes/processors to use for each | | | task. | +-------------------------+-----------------------------------------------+ | ``--preamble FILE`` | This option should be used when using DRMAA on| | | a HPC to load required module and set | | | environment variables. The content of the file| | | will be added between the 'shebang' line and | | | the tool command. | +-------------------------+-----------------------------------------------+ SHAPEIT options ---------------- .. table:: +-----------------------------+-------------------------------------------+ | Option | Description | +=============================+===========================================+ | ``--shapeit-bin BINARY`` | The SHAPEIT binary if it's not in the | | | path. | +-----------------------------+-------------------------------------------+ | ``--shapeit-thread INT`` | The number of thread for phasing. [``1``] | +-----------------------------+-------------------------------------------+ | ``--shapeit-extra OPTIONS`` | SHAPEIT extra parameters. Put extra | | | parameters between single or normal quotes| | | (*e.g.* ``--shapeit-extra '-- states 100 | | | --window 2'``). | +-----------------------------+-------------------------------------------+ Plink options -------------- .. table:: +------------------------+------------------------------------------------+ | Option | Description | +========================+================================================+ | ``--plink-bin BINARY`` | The Plink binary if it's not in the path. | +------------------------+------------------------------------------------+ IMPUTE2 autosomal reference ---------------------------- .. table:: +--------------------------------+----------------------------------------+ | Option | Description | +================================+========================================+ | ``--hap-template TEMPLATE`` | The template for IMPUTE2's haplotype | | | files (replace the chromosome number by| | | '``{chrom}``', *e.g.* | | | '``1000GP_{chrom}.hap.gz``'). | +--------------------------------+----------------------------------------+ | ``--legend-template TEMPLATE`` | The template for IMPUTE2's legend files| | | (replace the chromosome number by | | | '``{chrom}``', *e.g.* | | | '``1000GP_{chrom}.legend.gz``'). | +--------------------------------+----------------------------------------+ | ``--map-template TEMPLATE`` | The template for IMPUTE2's map files | | | (replace the chromosome number by | | | '``{chrom}``', *e.g.* | | | '``genetic_map_chr{chrom}.txt``'). | +--------------------------------+----------------------------------------+ | ``--sample-file FILE`` | The name of IMPUTE2's sample file. | +--------------------------------+----------------------------------------+ .. _params-chrom-x: IMPUTE2 chromosome X reference ------------------------------- .. table:: +--------------------------+----------------------------------------------+ | Option | Description | +==========================+==============================================+ | ``--hap-nonPAR FILE`` | The IMPUTE2's haplotype file for the | | | non-pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--hap-PAR1 FILE`` | The IMPUTE2's haplotype file for the first | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--hap-PAR2 FILE`` | The IMPUTE2's haplotype file for the second | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--legend-nonPAR FILE`` | The IMPUTE2's legend file for the | | | non-pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--legend-PAR1 FILE`` | The IMPUTE2's legend file for the first | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--legend-PAR2 FILE`` | The IMPUTE2's legend file for the second | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--map-nonPAR FILE`` | The IMPUTE2's map file for the | | | non-pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--map-PAR1 FILE`` | The IMPUTE2's map file for the first | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ | ``--map-PAR2 FILE`` | The IMPUTE2's map file for the second | | | pseudoautosomal region of chromosome 23. | +--------------------------+----------------------------------------------+ IMPUTE2 options ---------------- .. table:: +---------------------------------------+---------------------------------+ | Option | Description | +=======================================+=================================+ | ``--impute2-bin BINARY`` | The IMPUTE2 binary if it's not | | | in the path. | +---------------------------------------+---------------------------------+ | ``--segment-length BP`` | The length of a single segment | | | for imputation. [``5e+06``] | +---------------------------------------+---------------------------------+ | ``--filtering-rules RULE [RULE ...]`` | IMPUTE2 filtering rules | | | (optional). | +---------------------------------------+---------------------------------+ | ``--impute2-extra OPTIONS`` | IMPUTE2 extra parameters. Put | | | the extra parameters between | | | single or normal quotes (*e.g.* | | | ``--impute2-extra '-buffer 250 | | | -Ne 20000'``). | +---------------------------------------+---------------------------------+ .. _main-pipeline-merger-options: IMPUTE2 merger options ----------------------- .. table:: +-------------------------+-----------------------------------------------+ | Option | Description | +=========================+===============================================+ | ``--probability FLOAT`` | The probability threshold for no calls. | | | [``<0.9``] | +-------------------------+-----------------------------------------------+ | ``--completion FLOAT`` | The completion rate threshold for site | | | exclusion. [``<0.98``] | +-------------------------+-----------------------------------------------+ | ``--info FLOAT`` | The measure of the observed statistical | | | information associated with the allele | | | frequency estimate threshold for site | | | exclusion. [``<0.00``] | +-------------------------+-----------------------------------------------+ Automatic report options ------------------------- .. table:: +------------------------------------+------------------------------------+ | Option | Description | +====================================+====================================+ | ``--report-number NB`` | The report number. | | | [``genipe automatic report``] | +------------------------------------+------------------------------------+ | ``--report-title TITLE`` | The report title. [``genipe: | | | Automatic genome-wide imputation``]| +------------------------------------+------------------------------------+ | ``--report-author AUTHOR`` | The report author. [``Automatically| | | generated by genipe``] | +------------------------------------+------------------------------------+ | ``--report-background BACKGROUND`` | The report background section (can | | | either be a string or a file | | | containing the background. | | | [``General background``] | +------------------------------------+------------------------------------+