Pipeline for exome sequencing

Question

[kaushal2040]

Hello Forum,

What pipelines are available for exome sequencing analysis? Thanks for information.

[saadkhanwazir]

Dear All, I have started analyzing exome sequencing data, but can't find any a specific variant. I have data of exome, can anyone help me in this regard. Can you help me which software I should to use and and how to filter, nowadays I am using ion torrent. As I am new on this site, so sorry if I added the comments here

Answer 1

[Devon Ryan]

In addition to Ram's excellent answer, have a look at bcbio-nextgen and Brad Chapman's blog. The former demonstrates some effective methods for alignment and processing, the later describes a good number of comparisons that you should be familiar with if you want to really get into variant calling pipelines.

Answer 2

[Ram]

Pipelines are built from existing tools. Pipelines are usually customized. You will benefit from reading up on GATK's best practices, and exploring Galaxy documentation on if they have an exome sequencing tutorial.

[kaushal2040]

@Ram Thanks. I was also looking for any application/software available exome sequencing. I found one in bioconductor called CODEX.

Answer 3

[User 59]

Probably in need of an update, but not a bad overview of the steps: http://seqanswers.com/wiki/How-to/exome_analysis

Answer 4

[Karma]

The pipeline for exome analysis is well documented here exome_analysis

[Ram]

This is a bunch of links and sample commands, not a pipeline.