Post by mbyvcm on Oct 6, 2017 16:08:21 GMT
I have genome-wide summary stats and I am using 1000G European haplotypes. My command is:
gcta64 \
--bfile ./resources/ldref/1000G.EUR.all \
--cojo-file sumstats.txt \
--cojo-cond cond.snplist
--out test1
where cond.snplist is a single rsID.
GCTA runs without error. However, all conditional p-values (pC) are between 0 and 1.09e-35! Is this due to using small reference haplotype dataset?
gcta64 \
--bfile ./resources/ldref/1000G.EUR.all \
--cojo-file sumstats.txt \
--cojo-cond cond.snplist
--out test1
where cond.snplist is a single rsID.
GCTA runs without error. However, all conditional p-values (pC) are between 0 and 1.09e-35! Is this due to using small reference haplotype dataset?