Where should I go to download human SNP reference data ? hg18_unmasked.plusContam.fa

Question

[Ashley]

Dear all,

I want to call SNPs using Bis-SNP software, could you tell me where should I go?

BTW, http://epigenome.usc.edu/publicationdata/bissnp2011/easyUsage.html and http://epigenome.usc.edu/publicationdata/bissnp2011/utilies.html are not available.

Thanks for your help!

Answer 1

[ATpoint]

Whenever looking for software, first try conda and it is indeed available from that package manager. There is also a link to the current website of that tool. Also, as your title includes the reference genome hg18, you should know that this is an ancient version of the human genome. If you start a new project, start with hg38 and consider to read Which human reference genome should I use?

[Ashley]

I'm also want to use hg19 or hg38. However, I have to reproduce the result from other published paper first. Fortunately, they used hg18 and maq (2008 version). There are some many bugs ......