Question: Packages/modules for CNV, Indels, SNPs analysis
1
gravatar for Qingyang Xiao
4 months ago by
Qingyang Xiao100
Stockholm
Qingyang Xiao100 wrote:

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

Thank you again.

alignment snp sequence R genome • 260 views
ADD COMMENTlink modified 4 months ago by geocarvalho80 • written 4 months ago by Qingyang Xiao100

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?

ADD REPLYlink written 4 months ago by dariober9.2k
1
gravatar for Hussain Ather
4 months ago by
Hussain Ather860
National Institutes of Health, Bethesda, MD
Hussain Ather860 wrote:

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

ADD COMMENTlink written 4 months ago by Hussain Ather860
1
gravatar for geocarvalho
4 months ago by
geocarvalho80
Brazil/Recife
geocarvalho80 wrote:

See this repository:

ThousandVariantCallersRepo

ADD COMMENTlink written 4 months ago by geocarvalho80
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