Question: NGS Analysis Pipeline for Targeted Panel Data for SOMATIC tumours
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gravatar for always_learning
2.8 years ago by
Doha, Qatar
always_learning960 wrote:

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

panel ngs somatic • 1.5k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by always_learning960

Any update on this one ?

ADD REPLYlink written 2.7 years ago by always_learning960

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

ADD REPLYlink written 2.7 years ago by andrew.j.skelton735.6k
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gravatar for andrew.j.skelton73
2.8 years ago by
London
andrew.j.skelton735.6k wrote:

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

ADD COMMENTlink written 2.8 years ago by andrew.j.skelton735.6k

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

ADD REPLYlink written 2.8 years ago by always_learning960

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.

ADD REPLYlink written 2.8 years ago by andrew.j.skelton735.6k

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.

ADD REPLYlink written 2.8 years ago by andrew.j.skelton735.6k
0
gravatar for always_learning
2.8 years ago by
Doha, Qatar
always_learning960 wrote:

Any best practices available for Panel Sequencing data ?

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by always_learning960
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