In this video I will explain the next-generation sequencing (NGS) variant calling workflow.
Variant calling is performed to find mutations in diseases or cancers. It refers to the use of high-throughput sequencing technology to sequence and analyze the differences in the entire genome of an individual or population of a species, to obtain a large amount of genetic variation information, such as Single Nucleotide Polymorphism (SNP) , Insertion and deletion sites (InDel), structural variation sites (SV), copy number variation (CNV) etc.
First we have the raw reads that are in FastQ format and in order to check the quality of these reads we will perform a quality check on them using the FastQC tool. If the quality of these reads is good then we will perform alignment using any of the alignment tools available for instance Bowtie2, BWA.
If the quality of the reads is not good then first we will have to perform trimming and filtration on the raw reads in order to filter these reads using any of the tools that are available like Trimmomatic, Fastp, Cutadapt etc.
After alignment is performed we have mapped reads that are in the BAM/SAM file format. On these mapped reads, the base quality score recalibration is performed to get more accurate base qualities that will improve the accuracy of our variant calls. This is done using any of the tools available for example Bamutil or GATK. Then we move on to the variant calling.
The rest of the workflow will be explained in the next part of this video.
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