Question: Packages/modules for CNV, Indels, SNPs analysis
1
gravatar for Qingyang Xiao
10 months ago by
Qingyang Xiao120
Stockholm
Qingyang Xiao120 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 • 399 views
ADD COMMENTlink modified 10 months ago by geocarvalho80 • written 10 months ago by Qingyang Xiao120

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 10 months ago by dariober9.7k
1
gravatar for Hussain Ather
10 months ago by
Hussain Ather890
National Institutes of Health, Bethesda, MD
Hussain Ather890 wrote:

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

ADD COMMENTlink written 10 months ago by Hussain Ather890
1
gravatar for geocarvalho
10 months ago by
geocarvalho80
Brazil/Recife
geocarvalho80 wrote:

See this repository:

ThousandVariantCallersRepo

ADD COMMENTlink written 10 months ago by geocarvalho80
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