Question: How to get reference data for impute2 when imputing gwasdata
1
gravatar for liuyibin2005
3.1 years ago by
liuyibin20050 wrote:

Hi,everyone! I'm writting to ask you a question about a problem I met when I use Impute2 to impute my gwas data.It is one of the reference data ,"1000GP_Phase3_chr3.hap.gz "downloaded from the website https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html ,that is unable to gunzip. I have tried the 3rd time to download the whole file(10GB) and it comes the same.And I have wrote to the author but without reply.So I am here to plead for your help . How can I get the reference data in another way.

Thanks for your attention .Wish you have a good day.

snp • 840 views
ADD COMMENTlink written 3.1 years ago by liuyibin20050

Which platform are you doing this on? Should be possible on unix if there's enough disk space and memory. If you are able to download the file without any issues, split the file (split, head, etc), then concatenate the smaller files using cat or gzip -- I am assuming memory is the limiting factor.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by berge201580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1495 users visited in the last hour