Packages/modules for CNV, Indels, SNPs analysis

Hello! Can somebody kindly recommand some common and classical packages for targeted sequencing analysis of CNVs, Indels and SNPs?

Thank you again.

snp r sequence alignment genome

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updated 8.5 years ago by geocarvalho

• written 8.5 years ago by Qingyang Xiao

Hi- Are you interested in somatic variants (e.g. tumour vs normal detection) or germline variants (i.e. sample vs reference genome)? Also, when you say "analysis" do you mean going from raw data like fastq or bam files to detection and annotation? Or you have in mind some more specific analysis?

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written 8.5 years ago by dariober

2 answers

AnnTools https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289923/

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written 8.5 years ago by Hussain Ather

See this repository:

ThousandVariantCallersRepo

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written 8.5 years ago by geocarvalho

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