tag:blogger.com,1999:blog-6232819486261696035.post1129282058267664354..comments2023-09-25T09:01:44.323-05:00Comments on Getting Genetics Done: Randomly Select Subsets of Individuals from a Binary Pedigree .fam FileStephen Turnerhttp://www.blogger.com/profile/06656711316726116187noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-6232819486261696035.post-38268623174869627762010-11-24T13:59:05.451-06:002010-11-24T13:59:05.451-06:00Clarification
The MAF >40% SNPs that I removed...Clarification <br />The MAF >40% SNPs that I removed were limited to just the A/T, C/G SNPs on the 610quadAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-3467700659012574282010-11-24T13:55:32.293-06:002010-11-24T13:55:32.293-06:00Stephen,
I've imputed with the 1000 Genomes da...Stephen,<br />I've imputed with the 1000 Genomes data for our PGRN project as well.<br />One thing you should DEFINITELY keep in mind is to NOT use the 'compact' option in MACH. I tried it a couple of times out of curiosity and after giving Chrom 22 Step 1 > 2days it was apparent that it just wasn't going to happen.<br />I'm also a bit superstitious about running FROMDOS on everything as a precaution, there has definitely been a lot of time wasted around here just due to Windows leaving its dirty fingerprints on stuff. . .<br /><br />IIRC, RAM consumption varied from 2-6GB so make sure you've got plenty of overhead there.<br />I didn't have good luck running these as jobs on our cluster, maybe a memory management thing on the nodes, so I just resorted to running everything locally on my workstation leaving a few cores for normal daily activities. <br /><br />Stranding was also a bit of a pain. It's nice that the Illumina chip only have about 3500 A/T, C/G SNPs. I decided to remove everything that had a MAF >40% in either 1000 Genomes or my data set and spend the time doing a few PLINK merge-mode -7 tests before I was confident that I'd gotten the stranding worked out<br /><br />You've saved me more than a couple of times with your posts here, so I definitely owe ya. . .<br /><br />Thanks,<br />Mike BaldwinAnonymousnoreply@blogger.com