I have given 40 tumor samples to NGS for the analysis and I gave them a list of specific genes only do the sequencing for lets call that gene x1, x2, x3. Now they gave me the data in fastq format like sample1.fastq, sample2.fastq.... Now I want to check for mutations/SNPs in my gene x2.

I went through some online tutorials and did the following Aligned my sample1.fastq to x1.fasta and created a VCF file

Now I thinking to creat the same VCF file for all the samples and merge them. What analysis should I do next?

VCF, sequence, BAM, SAM, Linux, bwa, Bowtie2, SAM, tools, Adapter, Removal, cancer