Is there any user-friendly software for evaluation of whole exome sequence data?

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Christian Cole

Not that I'm aware of.

Whole exome/genome sequencing is a fast moving field at the moment so you're going to have get your hands dirty and learn to use tools like samtools mpileup and GATK

http://samtools.sourceforge.net/mpileup.shtml

http://www.broadinstitute.org/gatk/guide/best-practices

There is the GEMINI project, which helps a bit, but still not what I'd call 'user friendly'.

Anything that does call itself user friendly for WES/WGS is probably going to do a bad job as it won't deal properly with all the important descisions that need to be made when processing the data.

Victor Martinez-Glez

Unfortunately the only acceptable programs are not free, and for sure not user-friendly.

The problem with free software is that requires the use of several to perform the whole process, which makes it more complicated.

I recommend you read this paper: PMID: 23341494 Pabinger S, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2013

Razif R Gabdoulline

As realistic freeware options I would suggest:

LifeScope™ Genomic Analysis Software (for SOLiD sequencing data), and http://hugeseq.hugolam.com/ (Illumina). These are rather "one-click" pipelines, and need properly installed programs as well as batch system.

We also used a guide http://seqanswers.com/wiki/How-to/exome_analysis for creating our own analysis script.

Jeanette J Mccarthy

If you can get the data into .vcf format, Omicia (http://www.omicia.com) offers a very robust, user-friendly tool to analyze the data. Basic features are free, more advanced feature analysis costs ~$99 per genome.