Copy Number Variation Steps (CNVs) - detection step by step

Question

[elsayedhegazy]

Dear friends, I need to know the detailed steps of CNVs detection from NGS data (FASTQ , BAM, SAM or VCF). If i have one of these files what can i do to extract the copy number variation. i am not talking about tool names i need the algorithm steps.

Regards, elsayed

[Medhat]

Are you asking about the workflow how to get CNV from fastq file for example?

[elsayedhegazy]

Yes but with explanation of steps some like from FASTQ or VCF file we search for something after that we filter it using something

if you have one script code show all steps you are most welcome to post it here

Thanks a millions

Answer 1

[Medhat]

Ok, If the question is about workflow her it is:

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for algorithm you can read https://en.wikipedia.org/wiki/SNV_calling_from_NGS_data

and for in depth details: Review of alignment and SNP calling algorithms for next-generation sequencing data

A framework for variation discovery and genotyping using next-generation DNA sequencing data

for script you can follow this tutorial

Variant calling workflow - shell script

Workflow Or Tutorial For Snp Calling?

https://gencore.bio.nyu.edu/variant-calling-pipeline/

http://userweb.eng.gla.ac.uk/cosmika.goswami/snp_calling/SNPCalling.html

Good luck.

[elsayedhegazy]

Thanks a million medhat i will explore these links

Answer 2

[Chirag Nepal]

Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.

[elsayedhegazy]

Thanks Chirag, Still little bit confused these steps to run tools in proper way. My need is algorithm steps as concepts or theoretical steps - How to know this region contain CNV and how to extract it