tools

Small tools/pipelines commonly used by the RKJcollab.

liftover

Pipeline to run liftover using CrossMap - in development. Currently can do hg38 to hg19 for PLINK1.9 or bed input.

Examples:

bash liftover_plink.sh daisyask.bim /Users/slacksa/support

bash liftover_bed.sh T1DGC_saige_EUR_id.txt 1 2 14 /Users/slacksa/support

admixture

Initial version developed by Shane E. Ridoux.

TODOs:

• add documentation/use instructions here
• revisit and collapse 1-2 & 1-3
• make more files TMP only
• confirm MAF 0.1 at time LD prune merged input
• remove study-only Admixture step, shorten final script, & remove starting restriction to common variants?