NGS Analysis Pipeline for Targeted Panel Data for SOMATIC tumours

Question

[always_learning]

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

[always_learning]

Any update on this one ?

[andrew.j.skelton73]

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

Answer 1

[andrew.j.skelton73]

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

[always_learning]

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

[andrew.j.skelton73]

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.

[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.

Answer 2

[always_learning]

Any best practices available for Panel Sequencing data ?