Perfect gene investigation - ngs data clinical analysis step by step

Question

[dominik.saburo]

Hello there!

I have some doubts about my work with sequences and called gene variants generated in NGS.

When I am searching for potential pathogenic variant:

• I start from Illumina Variant Studio software and focuse on type of DNA change (f.e is it missense or synonymous).
• Next I'm checking the read depth and alternative read depth (if it is above 50% it sounds good to me)
• I also check the population frequencies in ExAC Browser and in UCSC database
• If there is an rs number I also try to find some information about clinical significance
• At the end I'm looking into the bam file by IGV software to see how this snp or mutation look like

That's in major what I am doing in my work :)

So my question is is there any better scheme or way to analyse my data?

Is there any way to successfull check my gene coverage? For this moment NGS report from Illumina doesn't suits me and I'm checking every exon by IGV software.

Have somebody worked in such medical science projects who has some good idea how to deal with such tasks as mine?

Maybe there is many better and more successfull ways to find gene mutations in NGS data?

Thaks for all replies!