Cohort Analysis Functions¶

List Variant

List Variant Genotype

List Variant Genotype Lite

List VCF

List VCF Lite

Collapsing

Collapsing Geno Lite

Collapsing VCF Lite

Fisher's Exact Test

Linear Regression

List Sibling Comp Het

List Trio

List Parental Mosaic

List Parent Comp Het

Generate Ped Map

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sample option is required to be used:

--sample: specify a sample file to include all your interested samples and their case/ctrl and family status.

file format: Family ID, Individual ID, Paternal ID, Maternal ID, Sex, Phenotype, Sample Type, Capture Kit (tab delimited)

Family ID: specify a family id or use the same value as Individual ID to indicate this sample used as a non family control or case
Individual ID: sample name
Paternal ID: sample name (father) or 0 (indicate not available)
Maternal ID: sample name (mother) or 0 (indicate not available)
Sex: 1=male,2=female
Phenotype: 1=control, 2=case
Sample Type & Capture Kit: please use the value form seqdb, including “N/A” for genome samples
Ex. /nfs/goldstein/software/atav_home/data/sample/ALS_1424_DukeGr_ctrl.txt

Note: please make sure all the controls are approved to use in your input sample file.