What is mutation calling in exome sequencing?

Question

[bioinforesearchquestions]

Dear All,

I am currently learning Exome sequencing. Can you please refer me some good research papers which deals with it.

After demultiplexing step, I have the fastq files for each samples. I am planning to do alignment first with human reference. After that I need to do mutation calling.

Is mutation calling different from variant calling?

What is the standard protocol to perform mutation calling analysis for exome sequencing?

[Sean Davis]

What is the experiment? Are you sequencing humans, or something else? Tumors? Germline? Families, or just individuals?

[bioinforesearchquestions]

Thanks for replying..I have been provided fastq files from human samples and asked me to work on standard exom_seq analysis and perform the mutation call.

Is there any difference between mutation calling and variant calling?

[poisonAlien]

Yeah. You need to be more specific. Protocols differ from what you are trying to do. If its tumors that your studying, this paper might be helpful for you. Expanding the computational toolbox for mining cancer genomes.

[bioinforesearchquestions]

Thanks for replying..I will go through this paper.

I am planning to do following steps

1. trimming the fastq files using trimmomatic
2. Aligning the reads against human reference genome then sort, deduplicate, recalibrate using GATK
3. Then planning to perform variant calling using GATK based on the bam generated in step 2
4. Then filter the variants
5. Then annotate the variants using ANNOVAR

Is my workflow correct or do I need to incorporate any other steps?

[Sean Davis]

Without knowing what the questions are, this sounds like a good general plan.