Compiling information from VCF files
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!
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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.