Galaxy |

plink (version 1.90b6.21+galaxy1)

Data inputs

Data inputs 0

Plink functions:

ID list functions:

ID extraction functions:

Chromosome(s):

Excludes all variants not on the listed chromosome(s). Can be listed as single chromsome, a hyphenated range, or comma separated list.

Exclude Chromosome(s):

Excludes all variants on the listed chromosome(s). Can be listed as single chromsome, a hyphenated range, or comma separated list.

Allow extra chromosomes:

Allows specified extra chromosomes/scaffolds not normally listed. ex. chr1_gl000191_random.

Autosome/unplaced exclusion:

SNP exclusive:

Single or multiple variant-based range window?:

Arbitrary thinning:

Missing Genotype Rates

Missing Genotype Rates 0

Allele Frequency

Allele Frequencies 0

hwe:

Set Hardy-Weinberg equilibrium tests

Filter on sex and/or founders:

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

For detailed usage notes, visit http://www.cog-genomics.org/plink/2.0/