Hello Experts and NGS Champions,
I know this might be old questions for you but Its been puzzling for me to have Analysis pipeline for Somatic cancer samples. I have fastq files for targeted panels and I want to process all the way upto VCF files for samples. If their is some accepted standard in NGS community for processing pipeline for such cases all the way to QC, Alignment and Alignment QC and then Variant Calling then Please suggest me some.
Thanks in advance and Sorry for lame simple questions.