Entering edit mode
4.2 years ago
sunnysean
▴
20
Hi, I am trying to use shapeit2 for imputation like this:
shapeit --input-bed test \
--input-map chr20.map \
--input-ref chr20.hap.gz, chr20.legend.gz, phase3.sample \
--output-max phased.haps, phased.sample
But shapeit2 always return "chr20.hap.gz is impossible to open, check file existence or reading permission". chr20.hap.gz are there, and I couldn't find any error with using "less -S chr20.hap.gz" to check it.
Thanks
Thank you! Great help!