How to analyze the generated VCF file, what to do if you have multiple VCF file for the same gene?
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
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