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• Impute2 Extractor - impute2-extractor

  • General options

  • Input files

  • Indexation options

  • Output options

  • Extraction options

Impute2 Extractor - impute2-extractor

Extract imputed markers located in a specific genomic region.

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’.