qctool.txt

Location of qctool -snp-stats results
=====================================

EGCUT, /data/anekal/EGCUT_INF.snp-stats

INTERVAL, /scratch/curated_genetic_data/reference_files/interval/

KORA, /data/jinhua/data/KORA/KORA.snp-stats.gz

STABILITY, /data/niceri/Stability_INF/SNPstats.zip

ORCADES, /data/jinhua/data/ORCADES

VIS, /data/jinhua/data/VIS

Pending cohorts
===============

NSPHS
STANLEY
MadCam
BioFinder

INFO cutoffs
============

NSPHS -- N/A as sequence data
STABILITY -- INFO > 0.4 as in sumstats (Min=0.4001)
STANLEY (lah1, swe6) -- INFO > 0.3 from sumstats as it appears to be r2hat
ORCADES -- INFO > 0.4 from sumstats where the minimum is 0.4
VIS -- INFO > 0.4 from sumstats as ORCADES
INTERVAL -- INFO > 0.3 as proper_info is NA
KORA -- INFO > 0.3 as for INTERVAL
EGCUT -- INFO > 0.4
MadCam -- INFO > 0.3
RECOMBINE -- INFO > 0.3
BioFInder -- NA