Association mapping using PLINK software

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.
Association mapping also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci(QTLs). In this video the software is demonstrated based on the study of Lumbar Disc Degenerative Disease in human. The study involves 58 SNPs,35 candidate genes in 342 individuals. To run this software the major requirements are three files namely ped, map and phenotype files. After running the software the final results are interpreted based on the P values obtained in the associated file. From this the gene (i.e) SNPs associated with the phenotype is found using the list of candidate genes. Finally the SNP location on the chromosome is showed in the Haploview software.

[@rizwanasyed14]

nice video, but i have question i have SNP data i want to know IBS, can you tell me input file and how to performed its little urgent. thanks in advance

[@GenomicsBootCamp]

For an IBS matrix in PLINK use the --distance option. The input files are standard PLINK, I have a lot of materials on this on my channel, see "Genomic data analysis for beginners" playlist

[@MSHAELTV]

hello
i need to to ex-plane me how to use command prompt plink software im beginner for this filed i really need to
how to used
how to run
how to merge data file
hot to prepare data file come from company to ped amd map file
could you make me clear video like this methodology
if i want to do genomic selection signature and GWAS

[@sergioleonelsimental8760]

hello could you give me the plink download link

[@shannusundar4066]

how to interpret the results obtained in pLink software

[@btnews2454]

Very good video learnt a lot How can I get the genotype of indian population

[@tarakachandrasekar2028]

good explanation.....can all sorts of human diseases be studied using this software?

[@nataliavaladaresdemoraes9454]

I am trying to save the PED files as Text tab delimited, with the extension .ped. However, the extension was not recognised as it shows a Text file in the directory. Anybody can help me to solve this? It happens to the Map files as well.

[@xiaohanwang1269]

You can download Notepad++, this software can open this kind of text document

[@krishnakumar-ou6ng]

nice video and explanation whether the software is popular among the common people

[@MrJGOTEN]

it is possible to do association mapping for diseases which are not inherited?

[@srividyanarasimhan9532]

is there any other stand-alone tool other than haploview, since it requires internet connection??

[@priyaj190]

nice video..the information about the video is very clear...

[@bewindouglas456]

Working of PLink software has been clearly explained...

[@poonkodibharathi9103]

nice video well explained.............

[@hashemin]

Very nice! the sound has some problems though!

[@prabakarankaruppasamy9902]

nice video...well explained video........

[@muttharasikavitha217]

nice video.Is there any expansion for PLINK?

[@a1b2c3d4e5f6g7h8i93]

you make it looks easy. thanks..

[@essakkiranimurugan5456]

well explained ..........nice video

[@Monisresidence]

no, there is no expansion for PLINK.

[@vadivelkulanthaivel3699]

good experience this video

[@srinivasannagarajan3001]

well explained video ..

[@iniyaal9831]

very useful video and well explained

[@SahithyaRaviraja]

how to compare the results?

[@sivakulasekarapaandian5996]

nice and well explained video

[@vinithas7933]

very informative video......

[@Monisresidence]

The p values obtained (i.e) at 1% or 5% significance is considered and the appropriate SNP ID is taken. These SNP ID's is then checked with the list of candidate genes provided and the GENE responsible for the DDD is found.

[@ramsureshkumar7824]

Monika kuppuraj

[@ramsureshkumar7824]

Monika can I get chance to talk. we are beginners and need help.

[@sountharya]

well explained video....

[@vigneshvicky3831]

clearly explained video...

[@sathyaseelanc5397]

nice video well explained.

[@biotechbalaji063]

more informative video

[@sountharya]

explained video.........

[@priyankarajendran9421]

very informative video

[@rihanasalma1245]

well explained video.very informative

[@rayho_]

very helpful-thank you!

[@abarnakirubalani2089]

well explained.

[@prabhajayaraman7961]

well explained

[@valarmathisri6684]

nice video

[@priyankapalaniswamy5433]

useful video.

[@jintuvijayan3008]

good work..

[@pradeepp6739]

nice video

[@sarankumar1667]

good

[@samyuktha1291]

Good

[@idalia5056]

Thanks, so is useful