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NGS Analysis Pipeline for Targeted Panel Data for SOMATIC tumours

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.

Thanks

somatic ngs panel
• 3,767 views • link
written by always_learning always_learning

VarScan or Samtools + BcfTools are probably your best option for any panels < 150MBases

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

2 answers

I'd usually say GATK, and MuTect2, however, I'm not too sure if they'd play well with Targeted Panels.

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Yes Since Panels have relatively high depth so I was just wondering how MuTect2, will work with Targeted Panels.

• 1 views • link
written by always_learning always_learning

It seems that 150M bases is the general rule of thumb - Anything more than that, and you should be fine, anything less then you'll have to look into other options.

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Also, I should mention that it's not really about the depth, as much as the "breadth" of data, if your panel surpasses 150M bases in length, then you should be fine.

• 1 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Any best practices available for Panel Sequencing data ?

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written by always_learning always_learning

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