Question: functional variant discovery after GATK variant calling
0
gravatar for moxu
2.5 years ago by
moxu440
moxu440 wrote:

I want to do variant calling from RNA-seq and I've followed GATK instruction at https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 and obtained the VCFs, one for a drug-sensitive cell line, the other for drug resistance cell line.

Now I want to

1) Find all those "meaningful" (e.g. indels, non-synonymous mutations) variants in each cell line, or at least sort the variants in terms of likely severity (e.g. rank importance of indels > missense/nonsense > synonymous > intergenic mutations) or validated clinical implications?

2) Find all those variants occur in the drug resistance cell line but not in the drug sensitive cell line, or vice versa, and rank these variants as stated in 1).

What are the best tools to do this?

snp genome gene • 747 views
ADD COMMENTlink modified 2.5 years ago by H.Hasani810 • written 2.5 years ago by moxu440
2
gravatar for WouterDeCoster
2.5 years ago by
Belgium
WouterDeCoster42k wrote:

I would suggest SnpSift and SnpEff.

ADD COMMENTlink written 2.5 years ago by WouterDeCoster42k

I am trying SnpEff and found some big problems: snpEff inappropriate interpretation of variants?. What's your experience in that aspect?

Thanks!

ADD REPLYlink written 2.4 years ago by moxu440
1
gravatar for H.Hasani
2.5 years ago by
H.Hasani810
Freiburg, Germany
H.Hasani810 wrote:

I'm all for VEP

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by H.Hasani810
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