Help to analyze Illumina HiSeq 2000 Human data

[kiradi]

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

[adamyao]

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

[Heisman]

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

[kiradi]

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?

[Heisman]

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.