PRSice2 - excluding MHC region

Nina Roth Mota

unread,

Feb 6, 2019, 1:29:10 PM2/6/19

to PRSice

Hi Sam and all,

I'm using PRSice2 and trying, with no luck, to exclude the MHC region from the analysis (former "remove.mhc T" command).

I'm adding the option

--x-range chr6:26000000-33000000

but then I get

Error in parse_args(OptionParser(option_list = option_list)) :

Error in getopt(spec = spec, opt = args) : long flag "x-range" is invalid

Execution halted

Can you help me spot what I might be doing wrong? It works great without this option...

Thank you in advance!

Best,

Nina

P.S. I'm working on LISA cluster (if this could be informative)

Laurie Hannigan

unread,

Mar 11, 2019, 7:56:21 AM3/11/19

to PRSice

Sam, I'm trying to do similar to Nina - I don't get an error but I don't get any SNPs excluded either. Can you provide any more info on formatting input for the --x-range flag?

Best,

Laurie

Sam Choi

unread,

Mar 12, 2019, 11:16:10 AM3/12/19

to PRSice

You should provide a genomic region for the --x-range flag

somethingl ike what Nina did should be the correct input

--x-range chr6:26000000-33000000

Reply all

Reply to author

Forward