is manual processing in variant calling pipleine important?

Question

[tariktj]

Hi all,

Given an automated variant calling pipeline, In which steps in this pipeline do you think that manual intervention would be important and can improve the quality of the final output? (excluding the pre-processing step of fastqc reads quality control).

would it be important for example to filter the variants in the resulting vfc files from gatk manually or can this be automated?

Can you please share with me some of your expertise in this matter?

many thanks !

Answer 1

[ivivek_ngs]

I have mentioned something to your earlier query in the variant calling thread. Take a look. Since you are doing it for the first time. It is always advisable to run each steps manually and do a thorough check of each of them with the plots so that you can get a hang of what exactly GATK is doing. It is a great resource but can be cumbersome owing to its thorough modules and too much of documentation. So it is advisable to check it carefully. As far filtering the vcf file, I would kindly ask you to look here as I mentioned under your comment.

Once you are aware of the entire workflow you can always make an automate workflow for future purposes. Good Luck!