Packages/modules for CNV, Indels, SNPs analysis

Question

[Qingyang Xiao]

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

Thank you again.

[dariober]

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?

Answer 1

[Hussain Ather]

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

Answer 2

[geocarvalho]

See this repository:

ThousandVariantCallersRepo