Question: Compiling information from VCF files
gravatar for errityf
24 months ago by
errityf0 wrote:

I am new to bioinformatics and would appreciate any help!

I am analysing data from IonTorrent of 52 genes from 20 samples. I am trying to detect somatic variants. I am comparing samtools, GATK and Galaxy.

I have generated VCF files for each of my 20 samples, I am now wondering what is the best way to compile these? I want to record the somatic variants in the different genes and compile the results into a table/chart. Is there a simpler way to do this than to manually go through all of the data?

I am also interested to know the best way to filter the variants that I have called.

Thank you!

ADD COMMENTlink written 24 months ago by errityf0

As far as I know, the variant calling pipeline that generates VCF files is different for somatic vs germline variant calls, in the sense that you may not be able to run a generic pipeline and then pick somatic variants after the fact. You should check your pipeline and also read up a bit on the parameter differences between the two pipelines.

ADD REPLYlink modified 24 months ago • written 24 months ago by Ram15k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 933 users visited in the last hour