Impute2 Extractor - Options and Parameters

General options

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.

Input files

Option Description
--impute2 FILE The output from IMPUTE2.

Indexation options

Option Description
--index Only perform the indexation.

Output options

Option Description
--out PREFIX The prefix of the output files. [impute2_extractor]
--format FORMAT [FORMAT ...] The output format. Can specify either ‘impute2’ for probabilities (same as impute2 format, i.e. 3 values per sample), ‘dosage’ for dosage values (one value between 0 and 2 by sample), ‘calls’ for hard calls, or ‘bed’ for Plink binary format (with hard calls). [impute2]
--long Write the output file in the long format (one line per sample per marker). This option is only compatible with the ‘calls’ and ‘dosage’ format (option ‘– format’).
--prob FLOAT The probability threshold used when creating a file in the dosage or call format. [0.9]

Extraction options

Option Description
--extract FILE File containing marker names to extract.
--genomic CHR:START-END The range to extract (e.g. 22 1000000 1500000). Can be use in combination with ‘--rate‘, ‘--maf‘ and ‘--info‘.
--maf FLOAT Extract markers with a minor allele frequency equal or higher than the specified threshold. Can be use in combination with ‘–rate’, ‘–info’ and ‘–genomic’.
--rate FLOAT Extract markers with a completion rate equal or higher to the specified threshold. Can be use in combination with ‘--maf‘, ‘--info‘ and ‘--genomic‘.
--info FLOAT Extract markers with an information equal or higher to the specified threshold. Can be use in combination with ‘--maf‘, ‘--rate‘ and ‘--genomic‘.