WGS downstream analysis

Question

[lz1903]

Hi community,

I am new to bioinformatics and whole genome sequencing. I have got WGS data and all up-stream analysis has been done. So in my hand, I have now annotated vcf files of each sample (with VEP). My question is that I wanted to see the overview of the seq data and if there are newly occurred muations. I also wanted to pick some variants for further analysis. I know all info are in the INFO field in the vcf. But I don't know where to start to filter vcf to get things I wanted. Is there any paper for down-stream analysis (which is based on the scientific purpose) or any general pipelines I can refer to?

Thanks! lz

[Pierre Lindenbaum]

if there are newly occurred muations.

what does it mean ? do you have trios ? are you looking for rare variants ?

I also wanted to pick some variants for further analysis.

what does it mean ?

[lz1903]

sorry I should have explain. My case is we have bulit a cancer cell model to recapture the whole transformation process starting from relatively healthy untransformed cells to malignant transformed tumor cells. We have done WGS on the control cell and tumor cell. So I wanted to compare the differences in the gemone between them. And I wanted to see during the transformation, is there muations (snv sv cnv)occured which could contribute to cell transformation. The vcf files contain all variants detected in the sample and I know where in the chromosome are those variants. It's just that there is a lot. I can't include all variants but pick some potent ones.

[zizigolu]

If you have two/some groups of samples to compare their whole genome, or you just have one group of samples, does not matter, if I were you, I would annotate vcf files with ANNOVAR because that is compatible with maftools R package. If you use maftools, you would be able to explore and visualise your data very well. For significantly/recurrently mutated genes, maftools has a function named oncodrive

If you have more that one group of samples, let's say, cancer versus normal, maftools has mafCompare function which gives you differentially mutated genes specific to each group

https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html

I really suggest you maftools

[lz1903]

Thank you so much for suggestion.