Help to analyze Illumina HiSeq 2000 Human data
 

Dear List,

I am new to NGS field. I have paired end sequenced Human Illumina HiSeq 2000 Data and have find SNP's out of that. And then I have to fidn out association of SNP's to a perticular trait. I would like to use open source tools such as bioconductor packages for data analysis. Hence, can somebody give me a functional pipeline for data analysis?

Thanking you in anticipation.

Regards,
Kiradi

Dear kiradi,

You can try VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) to see if it helps. It provides MegaQuery Download to download millions of annotated variants for NGS data in minutes.

Adam

Is it whole exome data? Regardless, you might want to read through this thread: http://seqanswers.com/forums/showthr...uencing+manual

Yes it is whole Exome data. I have gone through your documentation. it was really good. May I know is there any something similar packages available from bioconductor?

It's not my documentation, haha.

A lot of those things are available freely to anybody. For example, type in "donwload GATK" into google and you'll find the right link.