Question: What is best tool for Cohort data of DNA?
0
gravatar for 9521ljh
14 months ago by
9521ljh20
9521ljh20 wrote:

i have a hundred of DNA sequence samples of cancer patient. The data come from NGS.

Thus i am going to analysis it about Germline, Somatic, Mutation, Copy Number, Structural Variant ..and so on..

Please recommend the famous tools !

ADD COMMENTlink modified 14 months ago by manuel.belmadani1.2k • written 14 months ago by 9521ljh20
2

There is no gold standard to this. please read recent benchmarking papers to get an idea which tools and methods exist as well as blogs from people testing and comparing these tools. The search function here will also give you plenty of threads to read.

ADD REPLYlink modified 14 months ago • written 14 months ago by ATpoint40k
1
gravatar for manuel.belmadani
14 months ago by
Canada
manuel.belmadani1.2k wrote:

Most likely you'll want to use GATK at some point (possibly alongside other variant callers, but if you're starting off I'd say look at that first.) GATK is the"Genome Annotation Toolkit", it's a bundle of tools to deal with genomic data, generally for calling of genomic variants.

There's guides for the Best Practices pipelines for most of what you've mentioned here: https://software.broadinstitute.org/gatk/best-practices/

Freebayes would be another popular variant caller: https://github.com/ekg/freebayes, I usually run both GATK and Freebayes based pipelines and prioritize variants based on agreement.

ADD COMMENTlink modified 14 months ago • written 14 months ago by manuel.belmadani1.2k
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