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 !
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9521ljh •
1 answer
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.
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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.